Job ID = 6507871 SRX = SRX494952 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T13:01:26 prefetch.2.10.7: 1) Downloading 'SRR1198484'... 2020-06-26T13:01:26 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:05:54 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:05:54 prefetch.2.10.7: 1) 'SRR1198484' was downloaded successfully Read 33047917 spots for SRR1198484/SRR1198484.sra Written 33047917 spots for SRR1198484/SRR1198484.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: 00:04:43 33047917 reads; of these: 33047917 (100.00%) were unpaired; of these: 4343912 (13.14%) aligned 0 times 23795415 (72.00%) aligned exactly 1 time 4908590 (14.85%) aligned >1 times 86.86% overall alignment rate Time searching: 00:04:43 Overall time: 00:04:43 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] 5314997 / 28704005 = 0.1852 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 22:19:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494952/SRX494952.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494952/SRX494952.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494952/SRX494952.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494952/SRX494952.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 22:19:28: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:19:28: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:19:33: 1000000 INFO @ Fri, 26 Jun 2020 22:19:38: 2000000 INFO @ Fri, 26 Jun 2020 22:19:42: 3000000 INFO @ Fri, 26 Jun 2020 22:19:47: 4000000 INFO @ Fri, 26 Jun 2020 22:19:52: 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 @ Fri, 26 Jun 2020 22:19:57: 6000000 INFO @ Fri, 26 Jun 2020 22:19:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494952/SRX494952.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494952/SRX494952.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494952/SRX494952.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494952/SRX494952.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 22:19:58: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:19:58: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:20:02: 7000000 INFO @ Fri, 26 Jun 2020 22:20:03: 1000000 INFO @ Fri, 26 Jun 2020 22:20:07: 8000000 INFO @ Fri, 26 Jun 2020 22:20:09: 2000000 INFO @ Fri, 26 Jun 2020 22:20:13: 9000000 INFO @ Fri, 26 Jun 2020 22:20:14: 3000000 INFO @ Fri, 26 Jun 2020 22:20:18: 10000000 INFO @ Fri, 26 Jun 2020 22:20:19: 4000000 INFO @ Fri, 26 Jun 2020 22:20:23: 11000000 INFO @ Fri, 26 Jun 2020 22:20:24: 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 @ Fri, 26 Jun 2020 22:20:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494952/SRX494952.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494952/SRX494952.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494952/SRX494952.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494952/SRX494952.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 22:20:28: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:20:28: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:20:29: 12000000 INFO @ Fri, 26 Jun 2020 22:20:30: 6000000 INFO @ Fri, 26 Jun 2020 22:20:34: 1000000 INFO @ Fri, 26 Jun 2020 22:20:35: 13000000 INFO @ Fri, 26 Jun 2020 22:20:36: 7000000 INFO @ Fri, 26 Jun 2020 22:20:40: 2000000 INFO @ Fri, 26 Jun 2020 22:20:40: 14000000 INFO @ Fri, 26 Jun 2020 22:20:41: 8000000 INFO @ Fri, 26 Jun 2020 22:20:45: 3000000 INFO @ Fri, 26 Jun 2020 22:20:46: 15000000 INFO @ Fri, 26 Jun 2020 22:20:47: 9000000 INFO @ Fri, 26 Jun 2020 22:20:51: 4000000 INFO @ Fri, 26 Jun 2020 22:20:51: 16000000 INFO @ Fri, 26 Jun 2020 22:20:52: 10000000 INFO @ Fri, 26 Jun 2020 22:20:56: 5000000 INFO @ Fri, 26 Jun 2020 22:20:57: 17000000 INFO @ Fri, 26 Jun 2020 22:20:58: 11000000 INFO @ Fri, 26 Jun 2020 22:21:02: 6000000 INFO @ Fri, 26 Jun 2020 22:21:03: 18000000 INFO @ Fri, 26 Jun 2020 22:21:04: 12000000 INFO @ Fri, 26 Jun 2020 22:21:08: 7000000 INFO @ Fri, 26 Jun 2020 22:21:08: 19000000 INFO @ Fri, 26 Jun 2020 22:21:09: 13000000 INFO @ Fri, 26 Jun 2020 22:21:13: 8000000 INFO @ Fri, 26 Jun 2020 22:21:14: 20000000 INFO @ Fri, 26 Jun 2020 22:21:15: 14000000 INFO @ Fri, 26 Jun 2020 22:21:19: 9000000 INFO @ Fri, 26 Jun 2020 22:21:20: 21000000 INFO @ Fri, 26 Jun 2020 22:21:21: 15000000 INFO @ Fri, 26 Jun 2020 22:21:24: 10000000 INFO @ Fri, 26 Jun 2020 22:21:25: 22000000 INFO @ Fri, 26 Jun 2020 22:21:26: 16000000 INFO @ Fri, 26 Jun 2020 22:21:30: 11000000 INFO @ Fri, 26 Jun 2020 22:21:31: 23000000 INFO @ Fri, 26 Jun 2020 22:21:32: 17000000 INFO @ Fri, 26 Jun 2020 22:21:33: #1 tag size is determined as 35 bps INFO @ Fri, 26 Jun 2020 22:21:33: #1 tag size = 35 INFO @ Fri, 26 Jun 2020 22:21:33: #1 total tags in treatment: 23389008 INFO @ Fri, 26 Jun 2020 22:21:33: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:21:33: #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 22:21:34: #1 tags after filtering in treatment: 23389008 INFO @ Fri, 26 Jun 2020 22:21:34: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:21:34: #1 finished! INFO @ Fri, 26 Jun 2020 22:21:34: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:21:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:21:35: #2 number of paired peaks: 163 WARNING @ Fri, 26 Jun 2020 22:21:35: Fewer paired peaks (163) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 163 pairs to build model! INFO @ Fri, 26 Jun 2020 22:21:35: start model_add_line... INFO @ Fri, 26 Jun 2020 22:21:35: start X-correlation... INFO @ Fri, 26 Jun 2020 22:21:35: end of X-cor INFO @ Fri, 26 Jun 2020 22:21:35: #2 finished! INFO @ Fri, 26 Jun 2020 22:21:35: #2 predicted fragment length is 35 bps INFO @ Fri, 26 Jun 2020 22:21:35: #2 alternative fragment length(s) may be 2,35 bps INFO @ Fri, 26 Jun 2020 22:21:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494952/SRX494952.05_model.r WARNING @ Fri, 26 Jun 2020 22:21:35: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:21:35: #2 You may need to consider one of the other alternative d(s): 2,35 WARNING @ Fri, 26 Jun 2020 22:21:35: #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 22:21:35: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:21:35: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:21:36: 12000000 INFO @ Fri, 26 Jun 2020 22:21:37: 18000000 INFO @ Fri, 26 Jun 2020 22:21:42: 13000000 INFO @ Fri, 26 Jun 2020 22:21:42: 19000000 INFO @ Fri, 26 Jun 2020 22:21:47: 14000000 INFO @ Fri, 26 Jun 2020 22:21:47: 20000000 INFO @ Fri, 26 Jun 2020 22:21:52: 15000000 INFO @ Fri, 26 Jun 2020 22:21:53: 21000000 INFO @ Fri, 26 Jun 2020 22:21:58: 16000000 INFO @ Fri, 26 Jun 2020 22:21:59: 22000000 INFO @ Fri, 26 Jun 2020 22:22:04: 17000000 INFO @ Fri, 26 Jun 2020 22:22:05: 23000000 INFO @ Fri, 26 Jun 2020 22:22:07: #1 tag size is determined as 35 bps INFO @ Fri, 26 Jun 2020 22:22:07: #1 tag size = 35 INFO @ Fri, 26 Jun 2020 22:22:07: #1 total tags in treatment: 23389008 INFO @ Fri, 26 Jun 2020 22:22:07: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:22:07: #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 22:22:08: #1 tags after filtering in treatment: 23389008 INFO @ Fri, 26 Jun 2020 22:22:08: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:22:08: #1 finished! INFO @ Fri, 26 Jun 2020 22:22:08: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:22:08: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:22:09: #2 number of paired peaks: 163 WARNING @ Fri, 26 Jun 2020 22:22:09: Fewer paired peaks (163) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 163 pairs to build model! INFO @ Fri, 26 Jun 2020 22:22:09: start model_add_line... INFO @ Fri, 26 Jun 2020 22:22:09: start X-correlation... INFO @ Fri, 26 Jun 2020 22:22:10: end of X-cor INFO @ Fri, 26 Jun 2020 22:22:10: #2 finished! INFO @ Fri, 26 Jun 2020 22:22:10: #2 predicted fragment length is 35 bps INFO @ Fri, 26 Jun 2020 22:22:10: #2 alternative fragment length(s) may be 2,35 bps INFO @ Fri, 26 Jun 2020 22:22:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494952/SRX494952.10_model.r WARNING @ Fri, 26 Jun 2020 22:22:10: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:22:10: #2 You may need to consider one of the other alternative d(s): 2,35 WARNING @ Fri, 26 Jun 2020 22:22:10: #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 22:22:10: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:22:10: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:22:10: 18000000 INFO @ Fri, 26 Jun 2020 22:22:13: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:22:16: 19000000 INFO @ Fri, 26 Jun 2020 22:22:23: 20000000 INFO @ Fri, 26 Jun 2020 22:22:30: 21000000 INFO @ Fri, 26 Jun 2020 22:22:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494952/SRX494952.05_peaks.xls INFO @ Fri, 26 Jun 2020 22:22:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494952/SRX494952.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:22:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494952/SRX494952.05_summits.bed INFO @ Fri, 26 Jun 2020 22:22:35: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (7179 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:22:36: 22000000 INFO @ Fri, 26 Jun 2020 22:22:43: 23000000 INFO @ Fri, 26 Jun 2020 22:22:46: #1 tag size is determined as 35 bps INFO @ Fri, 26 Jun 2020 22:22:46: #1 tag size = 35 INFO @ Fri, 26 Jun 2020 22:22:46: #1 total tags in treatment: 23389008 INFO @ Fri, 26 Jun 2020 22:22:46: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:22:46: #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 22:22:46: #1 tags after filtering in treatment: 23389008 INFO @ Fri, 26 Jun 2020 22:22:46: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:22:46: #1 finished! INFO @ Fri, 26 Jun 2020 22:22:46: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:22:46: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:22:47: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:22:48: #2 number of paired peaks: 163 WARNING @ Fri, 26 Jun 2020 22:22:48: Fewer paired peaks (163) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 163 pairs to build model! INFO @ Fri, 26 Jun 2020 22:22:48: start model_add_line... INFO @ Fri, 26 Jun 2020 22:22:48: start X-correlation... INFO @ Fri, 26 Jun 2020 22:22:48: end of X-cor INFO @ Fri, 26 Jun 2020 22:22:48: #2 finished! INFO @ Fri, 26 Jun 2020 22:22:48: #2 predicted fragment length is 35 bps INFO @ Fri, 26 Jun 2020 22:22:48: #2 alternative fragment length(s) may be 2,35 bps INFO @ Fri, 26 Jun 2020 22:22:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494952/SRX494952.20_model.r WARNING @ Fri, 26 Jun 2020 22:22:48: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:22:48: #2 You may need to consider one of the other alternative d(s): 2,35 WARNING @ Fri, 26 Jun 2020 22:22:48: #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 22:22:48: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:22:48: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:23:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494952/SRX494952.10_peaks.xls INFO @ Fri, 26 Jun 2020 22:23:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494952/SRX494952.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:23:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494952/SRX494952.10_summits.bed INFO @ Fri, 26 Jun 2020 22:23:08: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1849 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 22:23:25: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:23:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494952/SRX494952.20_peaks.xls INFO @ Fri, 26 Jun 2020 22:23:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494952/SRX494952.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:23:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494952/SRX494952.20_summits.bed INFO @ Fri, 26 Jun 2020 22:23:46: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (201 records, 4 fields): 2 millis CompletedMACS2peakCalling