Job ID = 5791765 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 3,069,498 reads read : 6,138,996 reads written : 6,138,996 rm: cannot remove ‘[DSE]RR*’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:07 3069498 reads; of these: 3069498 (100.00%) were paired; of these: 177018 (5.77%) aligned concordantly 0 times 2546004 (82.95%) aligned concordantly exactly 1 time 346476 (11.29%) aligned concordantly >1 times ---- 177018 pairs aligned concordantly 0 times; of these: 77517 (43.79%) aligned discordantly 1 time ---- 99501 pairs aligned 0 times concordantly or discordantly; of these: 199002 mates make up the pairs; of these: 149470 (75.11%) aligned 0 times 21591 (10.85%) aligned exactly 1 time 27941 (14.04%) aligned >1 times 97.57% overall alignment rate Time searching: 00:02:07 Overall time: 00:02:07 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 72948 / 2966279 = 0.0246 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Apr 2020 10:46:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7741030/SRX7741030.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7741030/SRX7741030.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7741030/SRX7741030.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7741030/SRX7741030.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Wed, 22 Apr 2020 10:46:35: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:46:35: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:46:40: 1000000 INFO @ Wed, 22 Apr 2020 10:46:45: 2000000 INFO @ Wed, 22 Apr 2020 10:46:49: 3000000 INFO @ Wed, 22 Apr 2020 10:46:54: 4000000 INFO @ Wed, 22 Apr 2020 10:46:59: 5000000 INFO @ Wed, 22 Apr 2020 10:47:03: #1 tag size is determined as 80 bps INFO @ Wed, 22 Apr 2020 10:47:03: #1 tag size = 80 INFO @ Wed, 22 Apr 2020 10:47:03: #1 total tags in treatment: 2820749 INFO @ Wed, 22 Apr 2020 10:47:03: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:47:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 10:47:03: #1 tags after filtering in treatment: 2440626 INFO @ Wed, 22 Apr 2020 10:47:03: #1 Redundant rate of treatment: 0.13 INFO @ Wed, 22 Apr 2020 10:47:03: #1 finished! INFO @ Wed, 22 Apr 2020 10:47:03: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:47:03: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:47:03: #2 number of paired peaks: 184 WARNING @ Wed, 22 Apr 2020 10:47:03: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Wed, 22 Apr 2020 10:47:03: start model_add_line... INFO @ Wed, 22 Apr 2020 10:47:03: start X-correlation... INFO @ Wed, 22 Apr 2020 10:47:03: end of X-cor INFO @ Wed, 22 Apr 2020 10:47:03: #2 finished! INFO @ Wed, 22 Apr 2020 10:47:03: #2 predicted fragment length is 1 bps INFO @ Wed, 22 Apr 2020 10:47:03: #2 alternative fragment length(s) may be 1,13,41,62,65,70,75,125,148,182,196,221,254,290,322,345,348,365,396,415,439,443,449,466,482,501,530,558,571,576 bps INFO @ Wed, 22 Apr 2020 10:47:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7741030/SRX7741030.05_model.r WARNING @ Wed, 22 Apr 2020 10:47:03: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 10:47:03: #2 You may need to consider one of the other alternative d(s): 1,13,41,62,65,70,75,125,148,182,196,221,254,290,322,345,348,365,396,415,439,443,449,466,482,501,530,558,571,576 WARNING @ Wed, 22 Apr 2020 10:47:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 10:47:03: #3 Call peaks... INFO @ Wed, 22 Apr 2020 10:47:03: #3 Pre-compute pvalue-qvalue table... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Apr 2020 10:47:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7741030/SRX7741030.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7741030/SRX7741030.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7741030/SRX7741030.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7741030/SRX7741030.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Wed, 22 Apr 2020 10:47:05: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:47:05: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:47:06: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 10:47:08: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7741030/SRX7741030.05_peaks.xls INFO @ Wed, 22 Apr 2020 10:47:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7741030/SRX7741030.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 10:47:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7741030/SRX7741030.05_summits.bed INFO @ Wed, 22 Apr 2020 10:47:08: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:47:09: 1000000 INFO @ Wed, 22 Apr 2020 10:47:14: 2000000 INFO @ Wed, 22 Apr 2020 10:47:19: 3000000 INFO @ Wed, 22 Apr 2020 10:47:23: 4000000 INFO @ Wed, 22 Apr 2020 10:47:28: 5000000 INFO @ Wed, 22 Apr 2020 10:47:32: #1 tag size is determined as 80 bps INFO @ Wed, 22 Apr 2020 10:47:32: #1 tag size = 80 INFO @ Wed, 22 Apr 2020 10:47:32: #1 total tags in treatment: 2820749 INFO @ Wed, 22 Apr 2020 10:47:32: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:47:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 10:47:32: #1 tags after filtering in treatment: 2440626 INFO @ Wed, 22 Apr 2020 10:47:32: #1 Redundant rate of treatment: 0.13 INFO @ Wed, 22 Apr 2020 10:47:32: #1 finished! INFO @ Wed, 22 Apr 2020 10:47:32: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:47:32: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:47:32: #2 number of paired peaks: 184 WARNING @ Wed, 22 Apr 2020 10:47:32: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Wed, 22 Apr 2020 10:47:32: start model_add_line... INFO @ Wed, 22 Apr 2020 10:47:32: start X-correlation... INFO @ Wed, 22 Apr 2020 10:47:32: end of X-cor INFO @ Wed, 22 Apr 2020 10:47:32: #2 finished! INFO @ Wed, 22 Apr 2020 10:47:32: #2 predicted fragment length is 1 bps INFO @ Wed, 22 Apr 2020 10:47:32: #2 alternative fragment length(s) may be 1,13,41,62,65,70,75,125,148,182,196,221,254,290,322,345,348,365,396,415,439,443,449,466,482,501,530,558,571,576 bps INFO @ Wed, 22 Apr 2020 10:47:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7741030/SRX7741030.10_model.r WARNING @ Wed, 22 Apr 2020 10:47:32: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 10:47:32: #2 You may need to consider one of the other alternative d(s): 1,13,41,62,65,70,75,125,148,182,196,221,254,290,322,345,348,365,396,415,439,443,449,466,482,501,530,558,571,576 WARNING @ Wed, 22 Apr 2020 10:47:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 10:47:32: #3 Call peaks... INFO @ Wed, 22 Apr 2020 10:47:32: #3 Pre-compute pvalue-qvalue table... BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Apr 2020 10:47:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7741030/SRX7741030.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7741030/SRX7741030.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7741030/SRX7741030.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7741030/SRX7741030.bam'] # control file = None # effective genome size = 1.21e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Wed, 22 Apr 2020 10:47:35: #1 read tag files... INFO @ Wed, 22 Apr 2020 10:47:35: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 10:47:36: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 10:47:37: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7741030/SRX7741030.10_peaks.xls INFO @ Wed, 22 Apr 2020 10:47:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7741030/SRX7741030.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 10:47:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7741030/SRX7741030.10_summits.bed INFO @ Wed, 22 Apr 2020 10:47:37: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 10:47:40: 1000000 INFO @ Wed, 22 Apr 2020 10:47:44: 2000000 INFO @ Wed, 22 Apr 2020 10:47:49: 3000000 INFO @ Wed, 22 Apr 2020 10:47:54: 4000000 INFO @ Wed, 22 Apr 2020 10:47:58: 5000000 INFO @ Wed, 22 Apr 2020 10:48:02: #1 tag size is determined as 80 bps INFO @ Wed, 22 Apr 2020 10:48:02: #1 tag size = 80 INFO @ Wed, 22 Apr 2020 10:48:02: #1 total tags in treatment: 2820749 INFO @ Wed, 22 Apr 2020 10:48:02: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 10:48:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 10:48:02: #1 tags after filtering in treatment: 2440626 INFO @ Wed, 22 Apr 2020 10:48:02: #1 Redundant rate of treatment: 0.13 INFO @ Wed, 22 Apr 2020 10:48:02: #1 finished! INFO @ Wed, 22 Apr 2020 10:48:02: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 10:48:02: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 10:48:02: #2 number of paired peaks: 184 WARNING @ Wed, 22 Apr 2020 10:48:02: Fewer paired peaks (184) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 184 pairs to build model! INFO @ Wed, 22 Apr 2020 10:48:02: start model_add_line... INFO @ Wed, 22 Apr 2020 10:48:02: start X-correlation... INFO @ Wed, 22 Apr 2020 10:48:02: end of X-cor INFO @ Wed, 22 Apr 2020 10:48:02: #2 finished! INFO @ Wed, 22 Apr 2020 10:48:02: #2 predicted fragment length is 1 bps INFO @ Wed, 22 Apr 2020 10:48:02: #2 alternative fragment length(s) may be 1,13,41,62,65,70,75,125,148,182,196,221,254,290,322,345,348,365,396,415,439,443,449,466,482,501,530,558,571,576 bps INFO @ Wed, 22 Apr 2020 10:48:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7741030/SRX7741030.20_model.r WARNING @ Wed, 22 Apr 2020 10:48:02: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 10:48:02: #2 You may need to consider one of the other alternative d(s): 1,13,41,62,65,70,75,125,148,182,196,221,254,290,322,345,348,365,396,415,439,443,449,466,482,501,530,558,571,576 WARNING @ Wed, 22 Apr 2020 10:48:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 10:48:02: #3 Call peaks... INFO @ Wed, 22 Apr 2020 10:48:02: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 10:48:06: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 10:48:08: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7741030/SRX7741030.20_peaks.xls INFO @ Wed, 22 Apr 2020 10:48:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7741030/SRX7741030.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 10:48:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7741030/SRX7741030.20_summits.bed INFO @ Wed, 22 Apr 2020 10:48:08: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。