Job ID = 6497419 SRX = SRX494831 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T22:27:12 prefetch.2.10.7: 1) Downloading 'SRR1198363'... 2020-06-25T22:27:12 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:29:50 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:29:50 prefetch.2.10.7: 1) 'SRR1198363' was downloaded successfully Read 27717782 spots for SRR1198363/SRR1198363.sra Written 27717782 spots for SRR1198363/SRR1198363.sra 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: 00:04:12 27717782 reads; of these: 27717782 (100.00%) were unpaired; of these: 5104395 (18.42%) aligned 0 times 18377547 (66.30%) aligned exactly 1 time 4235840 (15.28%) aligned >1 times 81.58% overall alignment rate Time searching: 00:04:12 Overall time: 00:04:12 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 8 files... [bam_rmdupse_core] 3123645 / 22613387 = 0.1381 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 @ Fri, 26 Jun 2020 07:40:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494831/SRX494831.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494831/SRX494831.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494831/SRX494831.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494831/SRX494831.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 @ Fri, 26 Jun 2020 07:40:27: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:40:27: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:40:32: 1000000 INFO @ Fri, 26 Jun 2020 07:40:38: 2000000 INFO @ Fri, 26 Jun 2020 07:40:44: 3000000 INFO @ Fri, 26 Jun 2020 07:40:50: 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 @ Fri, 26 Jun 2020 07:40:55: 5000000 INFO @ Fri, 26 Jun 2020 07:40:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494831/SRX494831.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494831/SRX494831.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494831/SRX494831.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494831/SRX494831.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 @ Fri, 26 Jun 2020 07:40:57: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:40:57: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:41:02: 6000000 INFO @ Fri, 26 Jun 2020 07:41:03: 1000000 INFO @ Fri, 26 Jun 2020 07:41:09: 7000000 INFO @ Fri, 26 Jun 2020 07:41:10: 2000000 INFO @ Fri, 26 Jun 2020 07:41:15: 8000000 INFO @ Fri, 26 Jun 2020 07:41:17: 3000000 INFO @ Fri, 26 Jun 2020 07:41:22: 9000000 INFO @ Fri, 26 Jun 2020 07:41:23: 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 @ Fri, 26 Jun 2020 07:41:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494831/SRX494831.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494831/SRX494831.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494831/SRX494831.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494831/SRX494831.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 @ Fri, 26 Jun 2020 07:41:27: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:41:27: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:41:29: 10000000 INFO @ Fri, 26 Jun 2020 07:41:31: 5000000 INFO @ Fri, 26 Jun 2020 07:41:34: 1000000 INFO @ Fri, 26 Jun 2020 07:41:37: 11000000 INFO @ Fri, 26 Jun 2020 07:41:38: 6000000 INFO @ Fri, 26 Jun 2020 07:41:42: 2000000 INFO @ Fri, 26 Jun 2020 07:41:45: 12000000 INFO @ Fri, 26 Jun 2020 07:41:46: 7000000 INFO @ Fri, 26 Jun 2020 07:41:50: 3000000 INFO @ Fri, 26 Jun 2020 07:41:52: 13000000 INFO @ Fri, 26 Jun 2020 07:41:54: 8000000 INFO @ Fri, 26 Jun 2020 07:41:59: 4000000 INFO @ Fri, 26 Jun 2020 07:42:00: 14000000 INFO @ Fri, 26 Jun 2020 07:42:02: 9000000 INFO @ Fri, 26 Jun 2020 07:42:08: 15000000 INFO @ Fri, 26 Jun 2020 07:42:08: 5000000 INFO @ Fri, 26 Jun 2020 07:42:10: 10000000 INFO @ Fri, 26 Jun 2020 07:42:16: 16000000 INFO @ Fri, 26 Jun 2020 07:42:18: 6000000 INFO @ Fri, 26 Jun 2020 07:42:18: 11000000 INFO @ Fri, 26 Jun 2020 07:42:25: 17000000 INFO @ Fri, 26 Jun 2020 07:42:26: 12000000 INFO @ Fri, 26 Jun 2020 07:42:27: 7000000 INFO @ Fri, 26 Jun 2020 07:42:33: 18000000 INFO @ Fri, 26 Jun 2020 07:42:34: 13000000 INFO @ Fri, 26 Jun 2020 07:42:36: 8000000 INFO @ Fri, 26 Jun 2020 07:42:41: 19000000 INFO @ Fri, 26 Jun 2020 07:42:43: 14000000 INFO @ Fri, 26 Jun 2020 07:42:45: 9000000 INFO @ Fri, 26 Jun 2020 07:42:45: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 07:42:45: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 07:42:45: #1 total tags in treatment: 19489742 INFO @ Fri, 26 Jun 2020 07:42:45: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:42:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:42:46: #1 tags after filtering in treatment: 19489742 INFO @ Fri, 26 Jun 2020 07:42:46: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:42:46: #1 finished! INFO @ Fri, 26 Jun 2020 07:42:46: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:42:46: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:42:47: #2 number of paired peaks: 229 WARNING @ Fri, 26 Jun 2020 07:42:47: Fewer paired peaks (229) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 229 pairs to build model! INFO @ Fri, 26 Jun 2020 07:42:47: start model_add_line... INFO @ Fri, 26 Jun 2020 07:42:47: start X-correlation... INFO @ Fri, 26 Jun 2020 07:42:47: end of X-cor INFO @ Fri, 26 Jun 2020 07:42:47: #2 finished! INFO @ Fri, 26 Jun 2020 07:42:47: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 07:42:47: #2 alternative fragment length(s) may be 1,16,33,411,500,555,573,579 bps INFO @ Fri, 26 Jun 2020 07:42:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494831/SRX494831.05_model.r WARNING @ Fri, 26 Jun 2020 07:42:47: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:42:47: #2 You may need to consider one of the other alternative d(s): 1,16,33,411,500,555,573,579 WARNING @ Fri, 26 Jun 2020 07:42:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 07:42:47: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:42:47: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:42:51: 15000000 INFO @ Fri, 26 Jun 2020 07:42:54: 10000000 INFO @ Fri, 26 Jun 2020 07:42:59: 16000000 INFO @ Fri, 26 Jun 2020 07:43:03: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:43:07: 17000000 INFO @ Fri, 26 Jun 2020 07:43:11: 12000000 INFO @ Fri, 26 Jun 2020 07:43:15: 18000000 INFO @ Fri, 26 Jun 2020 07:43:20: 13000000 INFO @ Fri, 26 Jun 2020 07:43:23: 19000000 INFO @ Fri, 26 Jun 2020 07:43:24: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:43:27: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 07:43:27: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 07:43:27: #1 total tags in treatment: 19489742 INFO @ Fri, 26 Jun 2020 07:43:27: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:43:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:43:28: #1 tags after filtering in treatment: 19489742 INFO @ Fri, 26 Jun 2020 07:43:28: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:43:28: #1 finished! INFO @ Fri, 26 Jun 2020 07:43:28: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:43:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:43:29: 14000000 INFO @ Fri, 26 Jun 2020 07:43:29: #2 number of paired peaks: 229 WARNING @ Fri, 26 Jun 2020 07:43:29: Fewer paired peaks (229) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 229 pairs to build model! INFO @ Fri, 26 Jun 2020 07:43:29: start model_add_line... INFO @ Fri, 26 Jun 2020 07:43:29: start X-correlation... INFO @ Fri, 26 Jun 2020 07:43:29: end of X-cor INFO @ Fri, 26 Jun 2020 07:43:29: #2 finished! INFO @ Fri, 26 Jun 2020 07:43:29: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 07:43:29: #2 alternative fragment length(s) may be 1,16,33,411,500,555,573,579 bps INFO @ Fri, 26 Jun 2020 07:43:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494831/SRX494831.10_model.r WARNING @ Fri, 26 Jun 2020 07:43:29: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:43:29: #2 You may need to consider one of the other alternative d(s): 1,16,33,411,500,555,573,579 WARNING @ Fri, 26 Jun 2020 07:43:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 07:43:29: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:43:29: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:43:37: 15000000 INFO @ Fri, 26 Jun 2020 07:43:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494831/SRX494831.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:43:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494831/SRX494831.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:43:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494831/SRX494831.05_summits.bed INFO @ Fri, 26 Jun 2020 07:43:41: Done! pass1 - making usageList (0 chroms): 4 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:43:45: 16000000 INFO @ Fri, 26 Jun 2020 07:43:53: 17000000 BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:44:01: 18000000 INFO @ Fri, 26 Jun 2020 07:44:06: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:44:09: 19000000 INFO @ Fri, 26 Jun 2020 07:44:12: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 07:44:12: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 07:44:12: #1 total tags in treatment: 19489742 INFO @ Fri, 26 Jun 2020 07:44:12: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:44:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:44:13: #1 tags after filtering in treatment: 19489742 INFO @ Fri, 26 Jun 2020 07:44:13: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:44:13: #1 finished! INFO @ Fri, 26 Jun 2020 07:44:13: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:44:13: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:44:14: #2 number of paired peaks: 229 WARNING @ Fri, 26 Jun 2020 07:44:14: Fewer paired peaks (229) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 229 pairs to build model! INFO @ Fri, 26 Jun 2020 07:44:14: start model_add_line... INFO @ Fri, 26 Jun 2020 07:44:14: start X-correlation... INFO @ Fri, 26 Jun 2020 07:44:14: end of X-cor INFO @ Fri, 26 Jun 2020 07:44:14: #2 finished! INFO @ Fri, 26 Jun 2020 07:44:14: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 07:44:14: #2 alternative fragment length(s) may be 1,16,33,411,500,555,573,579 bps INFO @ Fri, 26 Jun 2020 07:44:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494831/SRX494831.20_model.r WARNING @ Fri, 26 Jun 2020 07:44:14: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:44:14: #2 You may need to consider one of the other alternative d(s): 1,16,33,411,500,555,573,579 WARNING @ Fri, 26 Jun 2020 07:44:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 07:44:14: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:44:14: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:44:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494831/SRX494831.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:44:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494831/SRX494831.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:44:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494831/SRX494831.10_summits.bed INFO @ Fri, 26 Jun 2020 07:44:23: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:44:49: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:45:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494831/SRX494831.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:45:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494831/SRX494831.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:45:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494831/SRX494831.20_summits.bed INFO @ Fri, 26 Jun 2020 07:45:06: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling