def gatk(timestamp, path_base, folder, samples, nproc, wt, q, genome_build, args):
args = args.split("|")
multithread = False
filt = "30"
if len(args) == 2:
if args[0] == "yes":
multithread = True
filt = args[1]
output = "results_gatk"
secure_mkdir(path_base + folder, output)
print "## Variang calling with GATK"
print "> Writing jobs for GATK..."
nproc, nchild, bsub_suffix = manager.get_bsub_arg(nproc, len(samples))
commands = list()
ksamp = sortbysize(samples)
proc_files = os.listdir(path_base + folder + "/results_sam2sortbam/")
for sample in ksamp:
in_file = path_base + folder + "/results_sam2sortbam/" + sample + ".sorted.bam"
if sample + ".sorted.bam" in proc_files:
C = gatk_commands(path_base + folder, sample, genome_build, multithread, filt)
commands.append("\n".join(C))
else:
print "Warning: [GATK] SORTED BAM output file not found -> " + in_file
create_scripts(nchild, commands, path_base, folder, output)
return submit_job_super("gatk", path_base + folder, wt, str(nproc), q, len(samples), bsub_suffix, nchild, timestamp)
def picardqc(timestamp, path_base, folder, samples, nproc, wt, q, annots, strand):
nstrand = {" --stranded=no":"NONE", " --stranded=yes":"FIRST_READ_TRANSCRIPTION_STRAND", " --stranded=no":"SECOND_READ_TRANSCRIPTION_STRAND"}
output = "results_picard"
secure_mkdir(path_base + folder, output)
print "## Alignment QC Picard-CollectRnaSeqMetrics"
print "> Writing jobs for Picard QC..."
nproc, nchild, bsub_suffix = manager.get_bsub_arg(nproc, len(samples))
commands = list()
ksamp = sortbysize(samples)
proc_files = os.listdir(path_base + folder + "/results_star/")
for sample in ksamp:
in_file = path_base + folder + "/results_star/" + sample + "_Aligned.out.sam"
if sample + "_Aligned.out.sam" in proc_files:
for i in range(len(config.nannots)):
annot = annots[i]
out_file = in_file.replace(".sam", "." + config.nannots[i] + ".qc").replace("results_star/", "results_picard/").replace("_Aligned.out", "")
call = "java -jar " + config.path_picard + "/CollectRnaSeqMetrics.jar REF_FLAT=" + annot + " STRAND_SPECIFICITY=" + nstrand[strand] + " INPUT=" + in_file + " OUTPUT=" + out_file
if i == (len(config.nannots)-1):
commands.append(call + sample_checker.replace("#FOLDER", path_base + folder + "/results_picard").replace("#SAMPLE", sample))
else:
commands.append(call)
else:
print "Warning: [Picard] STAR output file not found -> " + in_file
create_scripts(nchild, commands, path_base, folder, output)
return submit_job_super("picard", path_base + folder, wt, str(nproc), q, len(samples), bsub_suffix, nchild, timestamp)
def jsplice(timestamp, path_base, folder, samples, nproc, wt, q, genomebuild, pheno, extra_args, strand):
output_dir = path_base + folder + '/results_jsplice'
secure_mkdir(path_base + folder, 'results_jsplice')
print "## jSPLICE"
print "> Writing jobs for jSPLICE..."
nproc, nchild, bsub_suffix = manager.get_bsub_arg('1/NA/NA', len(samples))
commands = list()
ksamp = sortbysize(samples)
out = open(output_dir + '/expdesign.txt', 'w')
print >> out, '#exp\tcond\tjxnFile\tbamFile'
for sample in ksamp:
sj_file = path_base + folder + '/results_star/' + sample + '_SJ.out.tab' # Junction file created by STAR
sj_out_file = output_dir + '/' + sample + '.SJ.bed'
bam_file = path_base + folder + '/results_sam2sortbam/' + sample + '.sorted.bam' # BAM file created by STAR/Picard(AddOrReplaceReadGroups)
if os.path.exists(sj_file) and os.path.exists(bam_file) and len(pheno[sample].split(':'))==2:
command = 'python ' + config.path_jsplice + '/starJxn2bed.py -f ' + sj_file + ' -o '+ sj_out_file
commands.append(command + sample_checker.replace("#FOLDER", output_dir).replace("#SAMPLE", sample))
print >> out, '\t'.join([pheno[sample].split(':')[0], pheno[sample].split(':')[1], sj_out_file, bam_file])
else:
print "Warning: [JSPLICE] STAR output files not found -> " + sample
out.close()
if strand == " --stranded=no":
extra_args = '-s ' + extra_args
commands.append('python ' + config.path_jsplice + '/jSplice.py -d ' + output_dir + '/expdesign.txt -o ' + output_dir + ' -a '+ config.path_annotation.replace("#LABEL", genomebuild) + ' ' + extra_args)
create_scripts(nchild, commands, path_base, folder, 'results_jsplice')
return submit_job_super("jsplice", path_base + folder, wt, str(nproc), q, len(samples), bsub_suffix, nchild, timestamp)
def star(timestamp, path_base, folder, samples, nproc, wt, q, path_genome, star_params, tg):
output = "results_star"
secure_mkdir(path_base + folder, output)
print "## RNAseq alignment with STAR..."
print "> Writing jobs for STAR alignment..."
nproc, nchild, bsub_suffix = manager.get_bsub_arg(nproc, len(samples))
commands = list()
ksamp = sortbysize(samples)
for sample in ksamp:
gg = ""
files = samples[sample]
if not tg:
if len(files) == 2:
fn = files[0]
else:
fn = files[0] + " " + files[1]
if files[0].endswith(".fastq.gz"):
gg = " --readFilesCommand zcat"
else:
gg = " --readFilesCommand zcat"
g = path_base + folder + "/results_trimgalore/"
suf = ""
if not files[0].split("/")[-1].endswith(".gz"):
suf = ".gz"
if len(files) == 2:
fn = g + files[0].split("/")[-1] + suf
else:
fn = g + files[0].split("/")[-1] + suf + " " + g + files[1].split("/")[-1] + suf
command = config.path_star + " --quantMode TranscriptomeSAM GeneCounts --runThreadN " + str(nproc) + " --genomeDir " + path_genome
command = command + " --readFilesIn " + fn + " --outFileNamePrefix " + path_base + folder + "/results_star/" + sample + "_" + gg
if len(star_params) > 0:
command = command + star_params
commands.append(command + sample_checker.replace("#FOLDER", path_base + folder + "/results_star").replace("#SAMPLE", sample))
create_scripts(nchild, commands, path_base, folder, output)
return submit_job_super("star", path_base + folder, wt, str(nproc), q, len(samples), bsub_suffix, nchild, timestamp)
def starfusion(timestamp, path_base, folder, samples, nproc, wt, q, path_star_fusion, star_fusion_params, tg):
output = "results_star-fusion"
secure_mkdir(path_base + folder, output)
print "## Identification of gene fusions with star-fusion"
print "> Writing jobs for Star-Fusion..."
nproc, nchild, bsub_suffix = manager.get_bsub_arg(nproc, len(samples))
commands = list()
ksamp = sortbysize(samples)
for sample in ksamp:
files = samples[sample]
if not tg:
fn = files
else:
g = path_base + folder + "/results_trimgalore/"
suf = ""
if not files[0].split("/")[-1].endswith(".gz"):
suf = ".gz"
fn = [g + files[0].split("/")[-1] + suf, g + files[1].split("/")[-1] + suf]
prefix = path_base + folder + "/results_star-fusion/" + sample
call = config.path_starfusion + " --output_dir " + prefix + " --genome_lib_dir " + path_star_fusion + " --left_fq " + fn[0] + " --right_fq " + fn[1] + " --CPU " + str(nproc)
if len(star_fusion_params) > 0:
call = call + star_fusion_params
commands.append(call + sample_checker.replace("#FOLDER", path_base + folder + "/results_star-fusion").replace("#SAMPLE", sample))
create_scripts(nchild, commands, path_base, folder, output)
return submit_job_super("star-fusion", path_base + folder, wt, str(nproc), q, len(samples), bsub_suffix, nchild, timestamp)
def fastqc(timestamp, path_base, folder, samples, nproc, wt, q, tg):
########################################################################
## FastQC analysis
########################################################################
print "## QC: FastQC"
print "> Quality control with fastQC..."
output = "results_fastqc"
secure_mkdir(path_base + folder, "results_fastqc")
output_folder = path_base + folder + "/results_fastqc"
print "> Writing jobs for fastqc analysis..."
nproc, nchild, bsub_suffix = manager.get_bsub_arg(nproc, len(samples))
commands = list()
ksamp = sortbysize(samples)
for sample in ksamp:
files = samples[sample]
if not tg:
if len(files) == 4:
fnames = files[0] + " " + files[1]
else:
fnames = files[0]
else:
g = path_base + folder + "/results_trimgalore/"
suf = ""
if not files[0].split("/")[-1].endswith(".gz"):
suf = ".gz"
if len(files) == 4:
fnames = g + files[0].split("/")[-1] + suf + " " + g + files[1].split("/")[-1] + suf
else:
fnames = g + files[0].split("/")[-1] + suf
call = config.path_fastqc + " -q -o " + output_folder + " " + fnames
commands.append(call + sample_checker.replace("#FOLDER", output_folder).replace("#SAMPLE", sample))
create_scripts(nchild, commands, path_base, folder, output)
return submit_job_super("fastqc", path_base + folder, wt, str(nproc), q, len(samples), bsub_suffix, nchild, timestamp)
def trimgalore(timestamp, path_base, folder, samples, nproc, wt, q, extra_args):
########################################################################
## FastQC analysis
########################################################################
print "## Trim-galore: Quality and adapter trimming"
print "> Quality and adapter trimming with Trim Galore..."
output = "results_trimgalore"
secure_mkdir(path_base + folder, "results_trimgalore")
output_folder = path_base + folder + "/results_trimgalore"
print "> Writing jobs for TrimGalore analysis..."
nproc, nchild, bsub_suffix = manager.get_bsub_arg(nproc, len(samples))
commands = list()
ksamp = sortbysize(samples)
for sample in ksamp:
files = samples[sample]
if len(files) == 4:
args = extra_args + " --paired"
fnames = files[0] + " " + files[1]
else:
args = extra_args
fnames = files[0]
if (args != "") and (not args.startswith(" ")):
args = " " + args
call = config.path_trimgalore + args + " --gzip --path_to_cutadapt " + config.path_cutadapt + " -o " + output_folder + " " + fnames
call = call + sample_checker.replace("#FOLDER", output_folder).replace("#SAMPLE", sample) + "\n" + rename_tg_output(sample, files, path_base + folder)
commands.append(call)
create_scripts(nchild, commands, path_base, folder, output)
return submit_job_super("trimgalore", path_base + folder, wt, str(nproc), q, len(samples), bsub_suffix, nchild, timestamp)
def htseq(timestamp, path_base, folder, samples, path_annotation, nproc, wt, q,
mode, strand, countmode):
output = "results_htseq-" + mode
secure_mkdir(path_base + folder, output)
print "## HTseq-count"
print "> Writing jobs for HTseq-count " + mode + " analysis..."
nproc, nchild, bsub_suffix = manager.get_bsub_arg(nproc, len(samples))
commands = list()
ksamp = sortbysize(samples)
proc_files = os.listdir(path_base + folder + "/results_star/")
for sample in ksamp:
in_file = path_base + folder + "/results_star/" + sample + "_Aligned.out.sam"
if sample + "_Aligned.out.sam" in proc_files:
outputf = path_base + folder + "/results_htseq-" + mode + "/" + sample + ".tab"
if mode == "gene":
ld1 = config.path_htseq + strand + " -m " + countmode + " -q " + in_file + " " + path_annotation
else:
ld1 = config.path_htseq + strand + " -m " + countmode + " -i exon_id -q " + in_file + " " + path_annotation
call = ld1 + " > " + outputf
commands.append(
call +
sample_checker.replace("#FOLDER", path_base + folder + "/" +
output).replace("#SAMPLE", sample))
else:
print "Warning: [HTseq-" + mode + "] STAR output file not found -> " + in_file
create_scripts(nchild, commands, path_base, folder, output)
return submit_job_super("htseq-" + mode, path_base + folder, wt,
str(nproc), q, len(samples), bsub_suffix, nchild,
timestamp)
def starfusion(timestamp, path_base, folder, samples, nproc, wt, q,
genomebuild):
output = "results_star-fusion"
secure_mkdir(path_base + folder, output)
print "## Identification of gene fusions with star-fusion"
print "> Writing jobs for Star-Fusion..."
nproc, nchild, bsub_suffix = manager.get_bsub_arg(nproc, len(samples))
commands = list()
ksamp = sortbysize(samples)
proc_files = os.listdir(path_base + folder + "/results_star/")
ref_file = config.path_annotation.replace("#LABEL", genomebuild)
for sample in ksamp:
in_file1 = path_base + folder + "/results_star/" + sample + "_Chimeric.out.junction"
in_file2 = path_base + folder + "/results_star/" + sample + "_Chimeric.out.sam"
prefix = path_base + folder + "/results_star-fusion/" + sample
if os.path.exists(in_file1) and os.path.exists(in_file2):
call = config.path_starfusion + " -J " + in_file1 + " -S " + in_file2 + " -G " + ref_file + " --out_prefix " + prefix
commands.append(call + sample_checker.replace(
"#FOLDER", path_base + folder +
"/results_star-fusion").replace("#SAMPLE", sample))
else:
print "Warning: [Star-Fusion] STAR output file not found -> " + in_file1
create_scripts(nchild, commands, path_base, folder, output)
return submit_job_super("star-fusion", path_base + folder, wt, str(nproc),
q, len(samples), bsub_suffix, nchild, timestamp)
def kallisto(timestamp, path_base, folder, samples, path_index, bootstrap,
nproc, wt, q, tg):
output = "results_kallisto"
secure_mkdir(path_base + folder, "results_kallisto")
print "## RNAseq pseudoalignment with Kallisto"
# Estimate counts in single-end datasss
if len(samples[samples.keys()[0]]) == 2:
print "> Estimating average and STD of fragment lengh required by Kalisto on single-read data..."
outputT = path_base + folder + "/" + output + "/stats.txt"
tid, log = compute_mean_std(path_base, folder, samples, outputT, "1",
wt, q)
vcrparser.job_wait(log, 10)
f = open(outputT, 'r')
i = f.readline()
stats = dict()
for i in f:
i = i.strip("\n").split(" ")
stats[i[0]] = [i[2], i[3]]
f.close()
print "> Writing jobs for Kallisto pseudoalignment"
nproc, nchild, bsub_suffix = manager.get_bsub_arg(nproc, len(samples))
commands = list()
ksamp = sortbysize(samples)
for sample in ksamp:
files = samples[sample]
if not tg:
if len(files) == 4:
args = ""
fnames = files[0] + " " + files[1]
else:
args = " --single -l mean -s var".replace(
"mean", stats[sample][0]).replace("var", stats[sample][1])
fnames = files[0]
else:
g = path_base + folder + "/results_trimgalore/"
suf = ""
if not files[0].split("/")[-1].endswith(".gz"):
suf = ".gz"
if len(files) == 4:
args = ""
fnames = g + files[0].split(
"/")[-1] + suf + " " + g + files[1].split("/")[-1] + suf
else:
args = " --single -l mean -s var".replace(
"mean", stats[sample][0]).replace("var", stats[sample][1])
fnames = g + files[0].split("/")[-1] + suf
cmd = config.path_kallisto + " quant -b " + bootstrap + " -i " + path_index + " -o " + path_base + folder + "/results_kallisto/" + sample + args + " " + fnames
commands.append(
cmd + sample_checker.replace("#FOLDER", path_base + folder + "/" +
output).replace("#SAMPLE", sample))
create_scripts(nchild, commands, path_base, folder, output)
return submit_job_super("kallisto", path_base + folder, wt, str(nproc), q,
len(samples), bsub_suffix, nchild, timestamp)
def kallisto(timestamp, path_base, folder, samples, path_index, bootstrap, nproc, wt, q, tg):
output = "results_kallisto"
secure_mkdir(path_base + folder, "results_kallisto")
print "## RNAseq pseudoalignment with Kallisto"
# Estimate counts in single-end datasss
if len(samples[samples.keys()[0]]) == 2:
print "> Estimating average and STD of fragment lengh required by Kalisto on single-read data..."
outputT = path_base + folder + "/" + output + "/stats.txt"
tid,log = compute_mean_std(path_base, folder, samples, outputT, "1", wt, q)
vcrparser.job_wait(log, 10)
f = open(outputT,'r')
i = f.readline()
stats = dict()
for i in f:
i = i.strip("\n").split(" ")
stats[i[0]] = [i[2],i[3]]
f.close()
print "> Writing jobs for Kallisto pseudoalignment"
nproc, nchild, bsub_suffix = manager.get_bsub_arg(nproc, len(samples))
commands = list()
ksamp = sortbysize(samples)
for sample in ksamp:
files = samples[sample]
if not tg:
if len(files) == 4:
args = ""
fnames = files[0]+" "+files[1]
else:
args = " --single -l mean -s var".replace("mean", stats[sample][0]).replace("var", stats[sample][1])
fnames = files[0]
else:
g = path_base + folder + "/results_trimgalore/"
suf = ""
if not files[0].split("/")[-1].endswith(".gz"):
suf = ".gz"
if len(files) == 4:
args = ""
fnames = g + files[0].split("/")[-1] + suf + " " + g + files[1].split("/")[-1] + suf
else:
args = " --single -l mean -s var".replace("mean", stats[sample][0]).replace("var", stats[sample][1])
fnames = g + files[0].split("/")[-1] + suf
cmd = config.path_kallisto+" quant -b " + bootstrap + " -i " + path_index + " -o " + path_base+folder + "/results_kallisto/" + sample + args + " " + fnames
commands.append(cmd + sample_checker.replace("#FOLDER", path_base + folder + "/" + output).replace("#SAMPLE", sample))
create_scripts(nchild, commands, path_base, folder, output)
return submit_job_super("kallisto", path_base + folder, wt, str(nproc), q, len(samples), bsub_suffix, nchild, timestamp)
def sam2sortbam(timestamp, path_base, folder, samples, nproc, wt, q):
output = "results_sam2sortbam"
secure_mkdir(path_base + folder, output)
print "## SAM2SORTEDBAM"
print "> Writing jobs for SAM2SORTEDBAM..."
nproc, nchild, bsub_suffix = manager.get_bsub_arg(nproc, len(samples))
commands = list()
ksamp = sortbysize(samples)
proc_files = os.listdir(path_base + folder + "/results_star/")
for sample in ksamp:
in_file = path_base + folder + "/results_star/" + sample + "_Aligned.out.sam"
if sample + "_Aligned.out.sam" in proc_files:
out_file = path_base + folder + "/results_sam2sortbam/" + sample + ".sorted.bam"
com = "java -jar " + config.path_picard + "/AddOrReplaceReadGroups.jar I=" + in_file + " O=" + out_file +" SO=coordinate RGID=id RGLB=library RGPL=ILLUMINA RGPU=machine RGSM=sample 2> " + out_file + ".log"
commands.append(com + sample_checker.replace("#FOLDER", path_base + folder + "/results_sam2sortbam").replace("#SAMPLE", sample))
else:
print "Warning: [SAM2SORTEDBAM] STAR output file not found -> " + in_file
create_scripts(nchild, commands, path_base, folder, output)
return submit_job_super("sam2sortbam", path_base + folder, wt, str(nproc), q, len(samples), bsub_suffix, nchild, timestamp)
def varscan(timestamp, path_base, folder, samples, nproc, wt, q, genome_build, args):
ref = config.path_fasta.replace("#LABEL",genome_build)
output = "results_varscan"
secure_mkdir(path_base + folder, output)
print "## Variang calling with VARSCAN"
print "> Writing jobs for VARSCAN..."
nproc, nchild, bsub_suffix = manager.get_bsub_arg(nproc, len(samples))
commands = list()
ksamp = sortbysize(samples)
proc_files = os.listdir(path_base + folder + "/results_sam2sortbam/")
for sample in ksamp:
in_file = path_base + folder + "/results_sam2sortbam/" + sample + ".sorted.bam"
if sample + ".sorted.bam" in proc_files:
out_file = path_base + folder + "/results_varscan/" + sample + ".vcf"
com = config.path_samtools + " mpileup -B -f " + ref + " " + in_file + " | java -jar " + config.path_varscan + " mpileup2cns " + args + " > " + out_file
commands.append(com + sample_checker.replace("#FOLDER", path_base + folder + "/results_varscan").replace("#SAMPLE", sample))
else:
print "Warning: [VARSCAN] SORTED BAM output file not found -> " + in_file
create_scripts(nchild, commands, path_base, folder, output)
return submit_job_super("varscan", path_base + folder, wt, str(nproc), q, len(samples), bsub_suffix, nchild, timestamp)
def picard_IS(timestamp, path_base, folder, samples, nproc, wt, q):
output = "results_picard_IS"
secure_mkdir(path_base + folder, output)
print "## Picard-InsertSize"
print "> Writing jobs for Picard InsertSize..."
nproc, nchild, bsub_suffix = manager.get_bsub_arg(nproc, len(samples))
commands = list()
ksamp = sortbysize(samples)
proc_files = os.listdir(path_base + folder + "/results_sam2sortbam/")
for sample in ksamp:
in_file = path_base + folder + "/results_sam2sortbam/" + sample + ".sorted.bam"
if sample + ".sorted.bam" in proc_files:
for i in range(len(config.nannots)):
out_file = in_file.replace("results_sam2sortbam/", "results_picard_IS/").replace(".sorted.bam", "")
call = "java -jar " + config.path_picard + "/CollectInsertSizeMetrics.jar I="+in_file+" O="+out_file+".txt H="+out_file+".pdf"
commands.append(call + sample_checker.replace("#FOLDER", path_base + folder + "/results_picard_IS").replace("#SAMPLE", sample))
else:
print "Warning: [Picard] Sorted BAM file not found -> " + in_file
create_scripts(nchild, commands, path_base, folder, output)
return submit_job_super("picard_IS", path_base + folder, wt, str(nproc), q, len(samples), bsub_suffix, nchild, timestamp)
def starfusion(timestamp, path_base, folder, samples, nproc, wt, q, genomebuild):
output = "results_star-fusion"
secure_mkdir(path_base + folder, output)
print "## Identification of gene fusions with star-fusion"
print "> Writing jobs for Star-Fusion..."
nproc, nchild, bsub_suffix = manager.get_bsub_arg(nproc, len(samples))
commands = list()
ksamp = sortbysize(samples)
proc_files = os.listdir(path_base + folder + "/results_star/")
ref_file = config.path_annotation.replace("#LABEL", genomebuild)
for sample in ksamp:
in_file1 = path_base + folder + "/results_star/" + sample + "_Chimeric.out.junction"
in_file2 = path_base + folder + "/results_star/" + sample + "_Chimeric.out.sam"
prefix = path_base + folder + "/results_star-fusion/" + sample
if os.path.exists(in_file1) and os.path.exists(in_file2):
call = config.path_starfusion + " -J " + in_file1 + " -S " + in_file2 + " -G " + ref_file + " --out_prefix " + prefix
commands.append(call + sample_checker.replace("#FOLDER", path_base + folder + "/results_star-fusion").replace("#SAMPLE", sample))
else:
print "Warning: [Star-Fusion] STAR output file not found -> " + in_file1
create_scripts(nchild, commands, path_base, folder, output)
return submit_job_super("star-fusion", path_base + folder, wt, str(nproc), q, len(samples), bsub_suffix, nchild, timestamp)
def htseq(timestamp, path_base, folder, samples, path_annotation, nproc, wt, q, mode, strand, countmode):
output = "results_htseq-" + mode
secure_mkdir(path_base + folder, output)
print "## HTseq-count"
print "> Writing jobs for HTseq-count " + mode + " analysis..."
nproc, nchild, bsub_suffix = manager.get_bsub_arg(nproc, len(samples))
commands = list()
ksamp = sortbysize(samples)
proc_files = os.listdir(path_base + folder + "/results_star/")
for sample in ksamp:
in_file = path_base + folder + "/results_star/" + sample + "_Aligned.out.sam"
if sample + "_Aligned.out.sam" in proc_files:
outputf= path_base + folder + "/results_htseq-" + mode + "/" + sample + ".tab"
if mode == "gene":
ld1 = config.path_htseq + strand + " -m " + countmode + " -q " + in_file + " " + path_annotation
else:
ld1 = config.path_htseq + strand + " -m " + countmode + " -i exon_id -q " + in_file + " " + path_annotation
call = ld1 + " > " + outputf
commands.append(call + sample_checker.replace("#FOLDER", path_base + folder + "/" + output).replace("#SAMPLE", sample))
else:
print "Warning: [HTseq-" + mode + "] STAR output file not found -> " + in_file
create_scripts(nchild, commands, path_base, folder, output)
return submit_job_super("htseq-" + mode, path_base + folder, wt, str(nproc), q, len(samples), bsub_suffix, nchild, timestamp)
