Job ID = 6497416 SRX = SRX494828 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T21:49:11 prefetch.2.10.7: 1) Downloading 'SRR1198360'... 2020-06-25T21:49:42 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T21:51:18 prefetch.2.10.7: HTTPS download succeed 2020-06-25T21:51:18 prefetch.2.10.7: 1) 'SRR1198360' was downloaded successfully Read 29706298 spots for SRR1198360/SRR1198360.sra Written 29706298 spots for SRR1198360/SRR1198360.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: 00:04:38 29706298 reads; of these: 29706298 (100.00%) were unpaired; of these: 7084744 (23.85%) aligned 0 times 18663337 (62.83%) aligned exactly 1 time 3958217 (13.32%) aligned >1 times 76.15% overall alignment rate Time searching: 00:04:38 Overall time: 00:04:38 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] 2636481 / 22621554 = 0.1165 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 07:02:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494828/SRX494828.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494828/SRX494828.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494828/SRX494828.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494828/SRX494828.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 07:02:42: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:02:42: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:02:48: 1000000 INFO @ Fri, 26 Jun 2020 07:02:53: 2000000 INFO @ Fri, 26 Jun 2020 07:02:58: 3000000 INFO @ Fri, 26 Jun 2020 07:03:04: 4000000 INFO @ Fri, 26 Jun 2020 07:03:09: 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 07:03:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494828/SRX494828.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494828/SRX494828.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494828/SRX494828.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494828/SRX494828.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 07:03:12: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:03:12: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:03:14: 6000000 INFO @ Fri, 26 Jun 2020 07:03:18: 1000000 INFO @ Fri, 26 Jun 2020 07:03:19: 7000000 INFO @ Fri, 26 Jun 2020 07:03:24: 2000000 INFO @ Fri, 26 Jun 2020 07:03:25: 8000000 INFO @ Fri, 26 Jun 2020 07:03:30: 3000000 INFO @ Fri, 26 Jun 2020 07:03:31: 9000000 INFO @ Fri, 26 Jun 2020 07:03:36: 4000000 INFO @ Fri, 26 Jun 2020 07:03:37: 10000000 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 07:03:42: 5000000 INFO @ Fri, 26 Jun 2020 07:03:42: 11000000 INFO @ Fri, 26 Jun 2020 07:03:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494828/SRX494828.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494828/SRX494828.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494828/SRX494828.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494828/SRX494828.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 07:03:43: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:03:43: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:03:48: 6000000 INFO @ Fri, 26 Jun 2020 07:03:49: 12000000 INFO @ Fri, 26 Jun 2020 07:03:49: 1000000 INFO @ Fri, 26 Jun 2020 07:03:54: 7000000 INFO @ Fri, 26 Jun 2020 07:03:55: 13000000 INFO @ Fri, 26 Jun 2020 07:03:55: 2000000 INFO @ Fri, 26 Jun 2020 07:04:00: 8000000 INFO @ Fri, 26 Jun 2020 07:04:01: 14000000 INFO @ Fri, 26 Jun 2020 07:04:02: 3000000 INFO @ Fri, 26 Jun 2020 07:04:06: 9000000 INFO @ Fri, 26 Jun 2020 07:04:07: 15000000 INFO @ Fri, 26 Jun 2020 07:04:08: 4000000 INFO @ Fri, 26 Jun 2020 07:04:12: 10000000 INFO @ Fri, 26 Jun 2020 07:04:13: 16000000 INFO @ Fri, 26 Jun 2020 07:04:14: 5000000 INFO @ Fri, 26 Jun 2020 07:04:18: 11000000 INFO @ Fri, 26 Jun 2020 07:04:19: 17000000 INFO @ Fri, 26 Jun 2020 07:04:20: 6000000 INFO @ Fri, 26 Jun 2020 07:04:24: 12000000 INFO @ Fri, 26 Jun 2020 07:04:25: 18000000 INFO @ Fri, 26 Jun 2020 07:04:26: 7000000 INFO @ Fri, 26 Jun 2020 07:04:30: 13000000 INFO @ Fri, 26 Jun 2020 07:04:31: 19000000 INFO @ Fri, 26 Jun 2020 07:04:32: 8000000 INFO @ Fri, 26 Jun 2020 07:04:36: 14000000 INFO @ Fri, 26 Jun 2020 07:04:37: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 07:04:37: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 07:04:37: #1 total tags in treatment: 19985073 INFO @ Fri, 26 Jun 2020 07:04:37: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:04:37: #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 07:04:37: #1 tags after filtering in treatment: 19985073 INFO @ Fri, 26 Jun 2020 07:04:37: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:04:37: #1 finished! INFO @ Fri, 26 Jun 2020 07:04:37: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:04:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:04:38: 9000000 INFO @ Fri, 26 Jun 2020 07:04:39: #2 number of paired peaks: 178 WARNING @ Fri, 26 Jun 2020 07:04:39: Fewer paired peaks (178) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 178 pairs to build model! INFO @ Fri, 26 Jun 2020 07:04:39: start model_add_line... INFO @ Fri, 26 Jun 2020 07:04:39: start X-correlation... INFO @ Fri, 26 Jun 2020 07:04:39: end of X-cor INFO @ Fri, 26 Jun 2020 07:04:39: #2 finished! INFO @ Fri, 26 Jun 2020 07:04:39: #2 predicted fragment length is 35 bps INFO @ Fri, 26 Jun 2020 07:04:39: #2 alternative fragment length(s) may be 35,80,238,412,466,484,558,593 bps INFO @ Fri, 26 Jun 2020 07:04:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494828/SRX494828.05_model.r WARNING @ Fri, 26 Jun 2020 07:04:39: #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 07:04:39: #2 You may need to consider one of the other alternative d(s): 35,80,238,412,466,484,558,593 WARNING @ Fri, 26 Jun 2020 07:04:39: #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 07:04:39: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:04:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:04:42: 15000000 INFO @ Fri, 26 Jun 2020 07:04:44: 10000000 INFO @ Fri, 26 Jun 2020 07:04:48: 16000000 INFO @ Fri, 26 Jun 2020 07:04:50: 11000000 INFO @ Fri, 26 Jun 2020 07:04:54: 17000000 INFO @ Fri, 26 Jun 2020 07:04:56: 12000000 INFO @ Fri, 26 Jun 2020 07:05:00: 18000000 INFO @ Fri, 26 Jun 2020 07:05:02: 13000000 INFO @ Fri, 26 Jun 2020 07:05:06: 19000000 INFO @ Fri, 26 Jun 2020 07:05:08: 14000000 INFO @ Fri, 26 Jun 2020 07:05:11: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 07:05:11: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 07:05:11: #1 total tags in treatment: 19985073 INFO @ Fri, 26 Jun 2020 07:05:11: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:05:11: #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 07:05:12: #1 tags after filtering in treatment: 19985073 INFO @ Fri, 26 Jun 2020 07:05:12: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:05:12: #1 finished! INFO @ Fri, 26 Jun 2020 07:05:12: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:05:12: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:05:13: #2 number of paired peaks: 178 WARNING @ Fri, 26 Jun 2020 07:05:13: Fewer paired peaks (178) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 178 pairs to build model! INFO @ Fri, 26 Jun 2020 07:05:13: start model_add_line... INFO @ Fri, 26 Jun 2020 07:05:13: start X-correlation... INFO @ Fri, 26 Jun 2020 07:05:13: 15000000 INFO @ Fri, 26 Jun 2020 07:05:13: end of X-cor INFO @ Fri, 26 Jun 2020 07:05:13: #2 finished! INFO @ Fri, 26 Jun 2020 07:05:13: #2 predicted fragment length is 35 bps INFO @ Fri, 26 Jun 2020 07:05:13: #2 alternative fragment length(s) may be 35,80,238,412,466,484,558,593 bps INFO @ Fri, 26 Jun 2020 07:05:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494828/SRX494828.10_model.r WARNING @ Fri, 26 Jun 2020 07:05:13: #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 07:05:13: #2 You may need to consider one of the other alternative d(s): 35,80,238,412,466,484,558,593 WARNING @ Fri, 26 Jun 2020 07:05:13: #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 07:05:13: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:05:13: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:05:14: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:05:19: 16000000 INFO @ Fri, 26 Jun 2020 07:05:24: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:05:29: 18000000 INFO @ Fri, 26 Jun 2020 07:05:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494828/SRX494828.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:05:34: 19000000 INFO @ Fri, 26 Jun 2020 07:05:39: #1 tag size is determined as 36 bps INFO @ Fri, 26 Jun 2020 07:05:39: #1 tag size = 36 INFO @ Fri, 26 Jun 2020 07:05:39: #1 total tags in treatment: 19985073 INFO @ Fri, 26 Jun 2020 07:05:39: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:05:39: #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 07:05:40: #1 tags after filtering in treatment: 19985073 INFO @ Fri, 26 Jun 2020 07:05:40: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:05:40: #1 finished! INFO @ Fri, 26 Jun 2020 07:05:40: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:05:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:05:41: #2 number of paired peaks: 178 WARNING @ Fri, 26 Jun 2020 07:05:41: Fewer paired peaks (178) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 178 pairs to build model! INFO @ Fri, 26 Jun 2020 07:05:41: start model_add_line... INFO @ Fri, 26 Jun 2020 07:05:41: start X-correlation... INFO @ Fri, 26 Jun 2020 07:05:41: end of X-cor INFO @ Fri, 26 Jun 2020 07:05:41: #2 finished! INFO @ Fri, 26 Jun 2020 07:05:41: #2 predicted fragment length is 35 bps INFO @ Fri, 26 Jun 2020 07:05:41: #2 alternative fragment length(s) may be 35,80,238,412,466,484,558,593 bps INFO @ Fri, 26 Jun 2020 07:05:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494828/SRX494828.20_model.r WARNING @ Fri, 26 Jun 2020 07:05:42: #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 07:05:42: #2 You may need to consider one of the other alternative d(s): 35,80,238,412,466,484,558,593 WARNING @ Fri, 26 Jun 2020 07:05:42: #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 07:05:42: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:05:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:05:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494828/SRX494828.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:05:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494828/SRX494828.05_summits.bed INFO @ Fri, 26 Jun 2020 07:05:42: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (621 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:05:48: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:06:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494828/SRX494828.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:06:17: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:06:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494828/SRX494828.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:06:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494828/SRX494828.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:06:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494828/SRX494828.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:06:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494828/SRX494828.10_summits.bed INFO @ Fri, 26 Jun 2020 07:06:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494828/SRX494828.20_summits.bed INFO @ Fri, 26 Jun 2020 07:06:47: Done! INFO @ Fri, 26 Jun 2020 07:06:47: Done! BigWig に変換しました。 pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (48 records, 4 fields): 1 millis CompletedMACS2peakCalling pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (307 records, 4 fields): 25 millis CompletedMACS2peakCalling