Job ID = 5720339 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 40,364,270 reads read : 40,364,270 reads written : 40,364,270 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: 00:13:50 40364270 reads; of these: 40364270 (100.00%) were unpaired; of these: 1458746 (3.61%) aligned 0 times 29535976 (73.17%) aligned exactly 1 time 9369548 (23.21%) aligned >1 times 96.39% overall alignment rate Time searching: 00:13:50 Overall time: 00:13:50 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 9486867 / 38905524 = 0.2438 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 @ Thu, 16 Apr 2020 00:31:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7971803/SRX7971803.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7971803/SRX7971803.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7971803/SRX7971803.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7971803/SRX7971803.bam'] # control file = None # effective genome size = 9.00e+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 @ Thu, 16 Apr 2020 00:31:04: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:31:04: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:31:11: 1000000 INFO @ Thu, 16 Apr 2020 00:31:17: 2000000 INFO @ Thu, 16 Apr 2020 00:31:24: 3000000 INFO @ Thu, 16 Apr 2020 00:31:30: 4000000 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 @ Thu, 16 Apr 2020 00:31:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7971803/SRX7971803.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7971803/SRX7971803.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7971803/SRX7971803.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7971803/SRX7971803.bam'] # control file = None # effective genome size = 9.00e+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 @ Thu, 16 Apr 2020 00:31:34: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:31:34: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:31:37: 5000000 INFO @ Thu, 16 Apr 2020 00:31:41: 1000000 INFO @ Thu, 16 Apr 2020 00:31:44: 6000000 INFO @ Thu, 16 Apr 2020 00:31:48: 2000000 INFO @ Thu, 16 Apr 2020 00:31:51: 7000000 INFO @ Thu, 16 Apr 2020 00:31:55: 3000000 INFO @ Thu, 16 Apr 2020 00:31:58: 8000000 INFO @ Thu, 16 Apr 2020 00:32:02: 4000000 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 @ Thu, 16 Apr 2020 00:32:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7971803/SRX7971803.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7971803/SRX7971803.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7971803/SRX7971803.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7971803/SRX7971803.bam'] # control file = None # effective genome size = 9.00e+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 @ Thu, 16 Apr 2020 00:32:04: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:32:04: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:32:04: 9000000 INFO @ Thu, 16 Apr 2020 00:32:09: 5000000 INFO @ Thu, 16 Apr 2020 00:32:11: 10000000 INFO @ Thu, 16 Apr 2020 00:32:11: 1000000 INFO @ Thu, 16 Apr 2020 00:32:16: 6000000 INFO @ Thu, 16 Apr 2020 00:32:18: 11000000 INFO @ Thu, 16 Apr 2020 00:32:19: 2000000 INFO @ Thu, 16 Apr 2020 00:32:23: 7000000 INFO @ Thu, 16 Apr 2020 00:32:25: 12000000 INFO @ Thu, 16 Apr 2020 00:32:26: 3000000 INFO @ Thu, 16 Apr 2020 00:32:30: 8000000 INFO @ Thu, 16 Apr 2020 00:32:32: 13000000 INFO @ Thu, 16 Apr 2020 00:32:33: 4000000 INFO @ Thu, 16 Apr 2020 00:32:37: 9000000 INFO @ Thu, 16 Apr 2020 00:32:39: 14000000 INFO @ Thu, 16 Apr 2020 00:32:40: 5000000 INFO @ Thu, 16 Apr 2020 00:32:44: 10000000 INFO @ Thu, 16 Apr 2020 00:32:46: 15000000 INFO @ Thu, 16 Apr 2020 00:32:47: 6000000 INFO @ Thu, 16 Apr 2020 00:32:51: 11000000 INFO @ Thu, 16 Apr 2020 00:32:53: 16000000 INFO @ Thu, 16 Apr 2020 00:32:54: 7000000 INFO @ Thu, 16 Apr 2020 00:32:58: 12000000 INFO @ Thu, 16 Apr 2020 00:33:00: 17000000 INFO @ Thu, 16 Apr 2020 00:33:01: 8000000 INFO @ Thu, 16 Apr 2020 00:33:04: 13000000 INFO @ Thu, 16 Apr 2020 00:33:07: 18000000 INFO @ Thu, 16 Apr 2020 00:33:08: 9000000 INFO @ Thu, 16 Apr 2020 00:33:11: 14000000 INFO @ Thu, 16 Apr 2020 00:33:13: 19000000 INFO @ Thu, 16 Apr 2020 00:33:15: 10000000 INFO @ Thu, 16 Apr 2020 00:33:18: 15000000 INFO @ Thu, 16 Apr 2020 00:33:20: 20000000 INFO @ Thu, 16 Apr 2020 00:33:22: 11000000 INFO @ Thu, 16 Apr 2020 00:33:25: 16000000 INFO @ Thu, 16 Apr 2020 00:33:27: 21000000 INFO @ Thu, 16 Apr 2020 00:33:29: 12000000 INFO @ Thu, 16 Apr 2020 00:33:32: 17000000 INFO @ Thu, 16 Apr 2020 00:33:34: 22000000 INFO @ Thu, 16 Apr 2020 00:33:36: 13000000 INFO @ Thu, 16 Apr 2020 00:33:38: 18000000 INFO @ Thu, 16 Apr 2020 00:33:41: 23000000 INFO @ Thu, 16 Apr 2020 00:33:43: 14000000 INFO @ Thu, 16 Apr 2020 00:33:45: 19000000 INFO @ Thu, 16 Apr 2020 00:33:47: 24000000 INFO @ Thu, 16 Apr 2020 00:33:49: 15000000 INFO @ Thu, 16 Apr 2020 00:33:52: 20000000 INFO @ Thu, 16 Apr 2020 00:33:54: 25000000 INFO @ Thu, 16 Apr 2020 00:33:56: 16000000 INFO @ Thu, 16 Apr 2020 00:33:59: 21000000 INFO @ Thu, 16 Apr 2020 00:34:01: 26000000 INFO @ Thu, 16 Apr 2020 00:34:04: 17000000 INFO @ Thu, 16 Apr 2020 00:34:05: 22000000 INFO @ Thu, 16 Apr 2020 00:34:08: 27000000 INFO @ Thu, 16 Apr 2020 00:34:10: 18000000 INFO @ Thu, 16 Apr 2020 00:34:12: 23000000 INFO @ Thu, 16 Apr 2020 00:34:15: 28000000 INFO @ Thu, 16 Apr 2020 00:34:17: 19000000 INFO @ Thu, 16 Apr 2020 00:34:19: 24000000 INFO @ Thu, 16 Apr 2020 00:34:21: 29000000 INFO @ Thu, 16 Apr 2020 00:34:24: 20000000 INFO @ Thu, 16 Apr 2020 00:34:24: #1 tag size is determined as 76 bps INFO @ Thu, 16 Apr 2020 00:34:24: #1 tag size = 76 INFO @ Thu, 16 Apr 2020 00:34:24: #1 total tags in treatment: 29418657 INFO @ Thu, 16 Apr 2020 00:34:24: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:34:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 00:34:25: #1 tags after filtering in treatment: 29418657 INFO @ Thu, 16 Apr 2020 00:34:25: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:34:25: #1 finished! INFO @ Thu, 16 Apr 2020 00:34:25: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:34:25: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:34:26: 25000000 INFO @ Thu, 16 Apr 2020 00:34:27: #2 number of paired peaks: 148 WARNING @ Thu, 16 Apr 2020 00:34:27: Fewer paired peaks (148) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 148 pairs to build model! INFO @ Thu, 16 Apr 2020 00:34:27: start model_add_line... INFO @ Thu, 16 Apr 2020 00:34:27: start X-correlation... INFO @ Thu, 16 Apr 2020 00:34:27: end of X-cor INFO @ Thu, 16 Apr 2020 00:34:27: #2 finished! INFO @ Thu, 16 Apr 2020 00:34:27: #2 predicted fragment length is 1 bps INFO @ Thu, 16 Apr 2020 00:34:27: #2 alternative fragment length(s) may be 1,24,38,66,591 bps INFO @ Thu, 16 Apr 2020 00:34:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7971803/SRX7971803.05_model.r WARNING @ Thu, 16 Apr 2020 00:34:27: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 00:34:27: #2 You may need to consider one of the other alternative d(s): 1,24,38,66,591 WARNING @ Thu, 16 Apr 2020 00:34:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 00:34:27: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:34:27: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:34:31: 21000000 INFO @ Thu, 16 Apr 2020 00:34:32: 26000000 INFO @ Thu, 16 Apr 2020 00:34:38: 22000000 INFO @ Thu, 16 Apr 2020 00:34:39: 27000000 INFO @ Thu, 16 Apr 2020 00:34:45: 23000000 INFO @ Thu, 16 Apr 2020 00:34:46: 28000000 INFO @ Thu, 16 Apr 2020 00:34:51: 24000000 INFO @ Thu, 16 Apr 2020 00:34:52: 29000000 INFO @ Thu, 16 Apr 2020 00:34:55: #1 tag size is determined as 76 bps INFO @ Thu, 16 Apr 2020 00:34:55: #1 tag size = 76 INFO @ Thu, 16 Apr 2020 00:34:55: #1 total tags in treatment: 29418657 INFO @ Thu, 16 Apr 2020 00:34:55: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:34:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 00:34:56: #1 tags after filtering in treatment: 29418657 INFO @ Thu, 16 Apr 2020 00:34:56: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:34:56: #1 finished! INFO @ Thu, 16 Apr 2020 00:34:56: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:34:56: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:34:58: #2 number of paired peaks: 148 WARNING @ Thu, 16 Apr 2020 00:34:58: Fewer paired peaks (148) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 148 pairs to build model! INFO @ Thu, 16 Apr 2020 00:34:58: start model_add_line... INFO @ Thu, 16 Apr 2020 00:34:58: start X-correlation... INFO @ Thu, 16 Apr 2020 00:34:58: end of X-cor INFO @ Thu, 16 Apr 2020 00:34:58: #2 finished! INFO @ Thu, 16 Apr 2020 00:34:58: #2 predicted fragment length is 1 bps INFO @ Thu, 16 Apr 2020 00:34:58: #2 alternative fragment length(s) may be 1,24,38,66,591 bps INFO @ Thu, 16 Apr 2020 00:34:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7971803/SRX7971803.10_model.r WARNING @ Thu, 16 Apr 2020 00:34:58: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 00:34:58: #2 You may need to consider one of the other alternative d(s): 1,24,38,66,591 WARNING @ Thu, 16 Apr 2020 00:34:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 00:34:58: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:34:58: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:34:58: 25000000 INFO @ Thu, 16 Apr 2020 00:35:04: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:35:05: 26000000 INFO @ Thu, 16 Apr 2020 00:35:11: 27000000 INFO @ Thu, 16 Apr 2020 00:35:17: 28000000 INFO @ Thu, 16 Apr 2020 00:35:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7971803/SRX7971803.05_peaks.xls INFO @ Thu, 16 Apr 2020 00:35:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7971803/SRX7971803.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:35:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7971803/SRX7971803.05_summits.bed INFO @ Thu, 16 Apr 2020 00:35:21: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:35:24: 29000000 INFO @ Thu, 16 Apr 2020 00:35:27: #1 tag size is determined as 76 bps INFO @ Thu, 16 Apr 2020 00:35:27: #1 tag size = 76 INFO @ Thu, 16 Apr 2020 00:35:27: #1 total tags in treatment: 29418657 INFO @ Thu, 16 Apr 2020 00:35:27: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:35:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 00:35:27: #1 tags after filtering in treatment: 29418657 INFO @ Thu, 16 Apr 2020 00:35:27: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:35:27: #1 finished! INFO @ Thu, 16 Apr 2020 00:35:27: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:35:27: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:35:29: #2 number of paired peaks: 148 WARNING @ Thu, 16 Apr 2020 00:35:29: Fewer paired peaks (148) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 148 pairs to build model! INFO @ Thu, 16 Apr 2020 00:35:29: start model_add_line... INFO @ Thu, 16 Apr 2020 00:35:29: start X-correlation... INFO @ Thu, 16 Apr 2020 00:35:29: end of X-cor INFO @ Thu, 16 Apr 2020 00:35:29: #2 finished! INFO @ Thu, 16 Apr 2020 00:35:29: #2 predicted fragment length is 1 bps INFO @ Thu, 16 Apr 2020 00:35:29: #2 alternative fragment length(s) may be 1,24,38,66,591 bps INFO @ Thu, 16 Apr 2020 00:35:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7971803/SRX7971803.20_model.r WARNING @ Thu, 16 Apr 2020 00:35:29: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 00:35:29: #2 You may need to consider one of the other alternative d(s): 1,24,38,66,591 WARNING @ Thu, 16 Apr 2020 00:35:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 00:35:29: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:35:29: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:35:34: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:35:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7971803/SRX7971803.10_peaks.xls INFO @ Thu, 16 Apr 2020 00:35:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7971803/SRX7971803.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:35:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7971803/SRX7971803.10_summits.bed INFO @ Thu, 16 Apr 2020 00:35:51: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:36:07: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:36:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7971803/SRX7971803.20_peaks.xls INFO @ Thu, 16 Apr 2020 00:36:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7971803/SRX7971803.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:36:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7971803/SRX7971803.20_summits.bed INFO @ Thu, 16 Apr 2020 00:36:24: Done! pass1 - making usageList (0 chroms): 1 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。