Job ID = 10165638 SRX = SRX7505499 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-10-08T10:31:49 prefetch.2.10.7: 1) Downloading 'SRR10832157'... 2020-10-08T10:31:49 prefetch.2.10.7: Downloading via HTTPS... 2020-10-08T10:33:41 prefetch.2.10.7: HTTPS download succeed 2020-10-08T10:33:41 prefetch.2.10.7: 1) 'SRR10832157' was downloaded successfully 2020-10-08T10:33:41 prefetch.2.10.7: 'SRR10832157' has 0 unresolved dependencies Read 47572384 spots for SRR10832157/SRR10832157.sra Written 47572384 spots for SRR10832157/SRR10832157.sra fastq に変換しました。 bowtie でマッピング中... Your job 10165968 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:10:45 47572384 reads; of these: 47572384 (100.00%) were unpaired; of these: 2606284 (5.48%) aligned 0 times 36766932 (77.29%) aligned exactly 1 time 8199168 (17.24%) aligned >1 times 94.52% overall alignment rate Time searching: 00:10:45 Overall time: 00:10:45 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 20 files... [bam_rmdupse_core] 18227240 / 44966100 = 0.4054 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, 08 Oct 2020 19:54:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7505499/SRX7505499.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7505499/SRX7505499.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7505499/SRX7505499.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7505499/SRX7505499.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, 08 Oct 2020 19:54:15: #1 read tag files... INFO @ Thu, 08 Oct 2020 19:54:15: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 19:54:20: 1000000 INFO @ Thu, 08 Oct 2020 19:54:25: 2000000 INFO @ Thu, 08 Oct 2020 19:54:30: 3000000 INFO @ Thu, 08 Oct 2020 19:54:34: 4000000 INFO @ Thu, 08 Oct 2020 19:54:39: 5000000 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, 08 Oct 2020 19:54:44: 6000000 INFO @ Thu, 08 Oct 2020 19:54:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7505499/SRX7505499.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7505499/SRX7505499.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7505499/SRX7505499.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7505499/SRX7505499.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, 08 Oct 2020 19:54:45: #1 read tag files... INFO @ Thu, 08 Oct 2020 19:54:45: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 19:54:49: 7000000 INFO @ Thu, 08 Oct 2020 19:54:51: 1000000 INFO @ Thu, 08 Oct 2020 19:54:54: 8000000 INFO @ Thu, 08 Oct 2020 19:54:56: 2000000 INFO @ Thu, 08 Oct 2020 19:55:00: 9000000 INFO @ Thu, 08 Oct 2020 19:55:02: 3000000 INFO @ Thu, 08 Oct 2020 19:55:06: 10000000 INFO @ Thu, 08 Oct 2020 19:55:08: 4000000 INFO @ Thu, 08 Oct 2020 19:55:11: 11000000 INFO @ Thu, 08 Oct 2020 19:55:13: 5000000 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, 08 Oct 2020 19:55:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7505499/SRX7505499.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7505499/SRX7505499.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7505499/SRX7505499.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7505499/SRX7505499.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, 08 Oct 2020 19:55:15: #1 read tag files... INFO @ Thu, 08 Oct 2020 19:55:15: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 19:55:16: 12000000 INFO @ Thu, 08 Oct 2020 19:55:19: 6000000 INFO @ Thu, 08 Oct 2020 19:55:21: 1000000 INFO @ Thu, 08 Oct 2020 19:55:21: 13000000 INFO @ Thu, 08 Oct 2020 19:55:25: 7000000 INFO @ Thu, 08 Oct 2020 19:55:26: 2000000 INFO @ Thu, 08 Oct 2020 19:55:26: 14000000 INFO @ Thu, 08 Oct 2020 19:55:31: 8000000 INFO @ Thu, 08 Oct 2020 19:55:31: 3000000 INFO @ Thu, 08 Oct 2020 19:55:32: 15000000 INFO @ Thu, 08 Oct 2020 19:55:36: 9000000 INFO @ Thu, 08 Oct 2020 19:55:36: 4000000 INFO @ Thu, 08 Oct 2020 19:55:37: 16000000 INFO @ Thu, 08 Oct 2020 19:55:42: 10000000 INFO @ Thu, 08 Oct 2020 19:55:42: 5000000 INFO @ Thu, 08 Oct 2020 19:55:43: 17000000 INFO @ Thu, 08 Oct 2020 19:55:47: 6000000 INFO @ Thu, 08 Oct 2020 19:55:47: 11000000 INFO @ Thu, 08 Oct 2020 19:55:48: 18000000 INFO @ Thu, 08 Oct 2020 19:55:52: 7000000 INFO @ Thu, 08 Oct 2020 19:55:53: 12000000 INFO @ Thu, 08 Oct 2020 19:55:54: 19000000 INFO @ Thu, 08 Oct 2020 19:55:57: 8000000 INFO @ Thu, 08 Oct 2020 19:55:59: 20000000 INFO @ Thu, 08 Oct 2020 19:55:59: 13000000 INFO @ Thu, 08 Oct 2020 19:56:03: 9000000 INFO @ Thu, 08 Oct 2020 19:56:04: 21000000 INFO @ Thu, 08 Oct 2020 19:56:04: 14000000 INFO @ Thu, 08 Oct 2020 19:56:08: 10000000 INFO @ Thu, 08 Oct 2020 19:56:09: 22000000 INFO @ Thu, 08 Oct 2020 19:56:10: 15000000 INFO @ Thu, 08 Oct 2020 19:56:13: 11000000 INFO @ Thu, 08 Oct 2020 19:56:14: 23000000 INFO @ Thu, 08 Oct 2020 19:56:16: 16000000 INFO @ Thu, 08 Oct 2020 19:56:18: 12000000 INFO @ Thu, 08 Oct 2020 19:56:19: 24000000 INFO @ Thu, 08 Oct 2020 19:56:21: 17000000 INFO @ Thu, 08 Oct 2020 19:56:23: 13000000 INFO @ Thu, 08 Oct 2020 19:56:24: 25000000 INFO @ Thu, 08 Oct 2020 19:56:27: 18000000 INFO @ Thu, 08 Oct 2020 19:56:28: 14000000 INFO @ Thu, 08 Oct 2020 19:56:29: 26000000 INFO @ Thu, 08 Oct 2020 19:56:32: 19000000 INFO @ Thu, 08 Oct 2020 19:56:33: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 19:56:33: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 19:56:33: #1 total tags in treatment: 26738860 INFO @ Thu, 08 Oct 2020 19:56:33: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 19:56:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 19:56:33: 15000000 INFO @ Thu, 08 Oct 2020 19:56:34: #1 tags after filtering in treatment: 26738860 INFO @ Thu, 08 Oct 2020 19:56:34: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 19:56:34: #1 finished! INFO @ Thu, 08 Oct 2020 19:56:34: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 19:56:34: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 19:56:35: #2 number of paired peaks: 119 WARNING @ Thu, 08 Oct 2020 19:56:35: Fewer paired peaks (119) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 119 pairs to build model! INFO @ Thu, 08 Oct 2020 19:56:35: start model_add_line... INFO @ Thu, 08 Oct 2020 19:56:35: start X-correlation... INFO @ Thu, 08 Oct 2020 19:56:35: end of X-cor INFO @ Thu, 08 Oct 2020 19:56:35: #2 finished! INFO @ Thu, 08 Oct 2020 19:56:35: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 19:56:35: #2 alternative fragment length(s) may be 1,29,46,115,121,169,543,574 bps INFO @ Thu, 08 Oct 2020 19:56:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7505499/SRX7505499.05_model.r WARNING @ Thu, 08 Oct 2020 19:56:35: #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, 08 Oct 2020 19:56:35: #2 You may need to consider one of the other alternative d(s): 1,29,46,115,121,169,543,574 WARNING @ Thu, 08 Oct 2020 19:56:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 19:56:35: #3 Call peaks... INFO @ Thu, 08 Oct 2020 19:56:35: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 19:56:38: 20000000 INFO @ Thu, 08 Oct 2020 19:56:39: 16000000 INFO @ Thu, 08 Oct 2020 19:56:44: 21000000 INFO @ Thu, 08 Oct 2020 19:56:44: 17000000 INFO @ Thu, 08 Oct 2020 19:56:49: 22000000 INFO @ Thu, 08 Oct 2020 19:56:50: 18000000 INFO @ Thu, 08 Oct 2020 19:56:55: 23000000 INFO @ Thu, 08 Oct 2020 19:56:55: 19000000 INFO @ Thu, 08 Oct 2020 19:57:00: 20000000 INFO @ Thu, 08 Oct 2020 19:57:00: 24000000 INFO @ Thu, 08 Oct 2020 19:57:05: 21000000 INFO @ Thu, 08 Oct 2020 19:57:06: 25000000 INFO @ Thu, 08 Oct 2020 19:57:10: 22000000 INFO @ Thu, 08 Oct 2020 19:57:12: 26000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 19:57:14: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 19:57:15: 23000000 INFO @ Thu, 08 Oct 2020 19:57:16: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 19:57:16: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 19:57:16: #1 total tags in treatment: 26738860 INFO @ Thu, 08 Oct 2020 19:57:16: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 19:57:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 19:57:17: #1 tags after filtering in treatment: 26738860 INFO @ Thu, 08 Oct 2020 19:57:17: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 19:57:17: #1 finished! INFO @ Thu, 08 Oct 2020 19:57:17: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 19:57:17: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 19:57:18: #2 number of paired peaks: 119 WARNING @ Thu, 08 Oct 2020 19:57:18: Fewer paired peaks (119) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 119 pairs to build model! INFO @ Thu, 08 Oct 2020 19:57:18: start model_add_line... INFO @ Thu, 08 Oct 2020 19:57:18: start X-correlation... INFO @ Thu, 08 Oct 2020 19:57:18: end of X-cor INFO @ Thu, 08 Oct 2020 19:57:18: #2 finished! INFO @ Thu, 08 Oct 2020 19:57:18: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 19:57:18: #2 alternative fragment length(s) may be 1,29,46,115,121,169,543,574 bps INFO @ Thu, 08 Oct 2020 19:57:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7505499/SRX7505499.10_model.r WARNING @ Thu, 08 Oct 2020 19:57:18: #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, 08 Oct 2020 19:57:18: #2 You may need to consider one of the other alternative d(s): 1,29,46,115,121,169,543,574 WARNING @ Thu, 08 Oct 2020 19:57:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 19:57:18: #3 Call peaks... INFO @ Thu, 08 Oct 2020 19:57:18: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 19:57:20: 24000000 INFO @ Thu, 08 Oct 2020 19:57:25: 25000000 INFO @ Thu, 08 Oct 2020 19:57:30: 26000000 INFO @ Thu, 08 Oct 2020 19:57:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7505499/SRX7505499.05_peaks.xls INFO @ Thu, 08 Oct 2020 19:57:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7505499/SRX7505499.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 19:57:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7505499/SRX7505499.05_summits.bed INFO @ Thu, 08 Oct 2020 19:57:32: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 19:57:34: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 19:57:34: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 19:57:34: #1 total tags in treatment: 26738860 INFO @ Thu, 08 Oct 2020 19:57:34: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 19:57:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 19:57:34: #1 tags after filtering in treatment: 26738860 INFO @ Thu, 08 Oct 2020 19:57:34: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 19:57:34: #1 finished! INFO @ Thu, 08 Oct 2020 19:57:34: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 19:57:34: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 19:57:36: #2 number of paired peaks: 119 WARNING @ Thu, 08 Oct 2020 19:57:36: Fewer paired peaks (119) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 119 pairs to build model! INFO @ Thu, 08 Oct 2020 19:57:36: start model_add_line... INFO @ Thu, 08 Oct 2020 19:57:36: start X-correlation... INFO @ Thu, 08 Oct 2020 19:57:36: end of X-cor INFO @ Thu, 08 Oct 2020 19:57:36: #2 finished! INFO @ Thu, 08 Oct 2020 19:57:36: #2 predicted fragment length is 1 bps INFO @ Thu, 08 Oct 2020 19:57:36: #2 alternative fragment length(s) may be 1,29,46,115,121,169,543,574 bps INFO @ Thu, 08 Oct 2020 19:57:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7505499/SRX7505499.20_model.r WARNING @ Thu, 08 Oct 2020 19:57:36: #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, 08 Oct 2020 19:57:36: #2 You may need to consider one of the other alternative d(s): 1,29,46,115,121,169,543,574 WARNING @ Thu, 08 Oct 2020 19:57:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 19:57:36: #3 Call peaks... INFO @ Thu, 08 Oct 2020 19:57:36: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 19:57:57: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 19:58:14: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 19:58:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7505499/SRX7505499.10_peaks.xls INFO @ Thu, 08 Oct 2020 19:58:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7505499/SRX7505499.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 19:58:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7505499/SRX7505499.10_summits.bed INFO @ Thu, 08 Oct 2020 19:58:14: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 19:58:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7505499/SRX7505499.20_peaks.xls INFO @ Thu, 08 Oct 2020 19:58:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7505499/SRX7505499.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 19:58:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7505499/SRX7505499.20_summits.bed INFO @ Thu, 08 Oct 2020 19:58:31: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling