Job ID = 14157860 SRX = SRX10569196 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2021-12-08T02:43:04 prefetch.2.10.7: 1) Downloading 'SRR14202296'... 2021-12-08T02:43:04 prefetch.2.10.7: Downloading via HTTPS... 2021-12-08T02:58:43 prefetch.2.10.7: HTTPS download succeed 2021-12-08T02:58:43 prefetch.2.10.7: 1) 'SRR14202296' was downloaded successfully 2021-12-08T02:58:43 prefetch.2.10.7: 'SRR14202296' has 0 unresolved dependencies Read 27302513 spots for SRR14202296/SRR14202296.sra Written 27302513 spots for SRR14202296/SRR14202296.sra fastq に変換しました。 bowtie でマッピング中... Your job 14158066 ("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: 00:08:53 27302513 reads; of these: 27302513 (100.00%) were unpaired; of these: 9581105 (35.09%) aligned 0 times 14250369 (52.19%) aligned exactly 1 time 3471039 (12.71%) aligned >1 times 64.91% overall alignment rate Time searching: 00:08:53 Overall time: 00:08:53 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] 2424499 / 17721408 = 0.1368 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 12:14:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10569196/SRX10569196.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10569196/SRX10569196.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10569196/SRX10569196.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10569196/SRX10569196.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 @ Wed, 08 Dec 2021 12:14:52: #1 read tag files... INFO @ Wed, 08 Dec 2021 12:14:52: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 12:14:59: 1000000 INFO @ Wed, 08 Dec 2021 12:15:06: 2000000 INFO @ Wed, 08 Dec 2021 12:15:12: 3000000 INFO @ Wed, 08 Dec 2021 12:15:19: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 12:15:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10569196/SRX10569196.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10569196/SRX10569196.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10569196/SRX10569196.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10569196/SRX10569196.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 @ Wed, 08 Dec 2021 12:15:22: #1 read tag files... INFO @ Wed, 08 Dec 2021 12:15:22: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 12:15:26: 5000000 INFO @ Wed, 08 Dec 2021 12:15:29: 1000000 INFO @ Wed, 08 Dec 2021 12:15:34: 6000000 INFO @ Wed, 08 Dec 2021 12:15:36: 2000000 INFO @ Wed, 08 Dec 2021 12:15:41: 7000000 INFO @ Wed, 08 Dec 2021 12:15:43: 3000000 INFO @ Wed, 08 Dec 2021 12:15:48: 8000000 INFO @ Wed, 08 Dec 2021 12:15:49: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 08 Dec 2021 12:15:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10569196/SRX10569196.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10569196/SRX10569196.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10569196/SRX10569196.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10569196/SRX10569196.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 @ Wed, 08 Dec 2021 12:15:52: #1 read tag files... INFO @ Wed, 08 Dec 2021 12:15:52: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 12:15:56: 9000000 INFO @ Wed, 08 Dec 2021 12:15:56: 5000000 INFO @ Wed, 08 Dec 2021 12:15:59: 1000000 INFO @ Wed, 08 Dec 2021 12:16:03: 10000000 INFO @ Wed, 08 Dec 2021 12:16:03: 6000000 INFO @ Wed, 08 Dec 2021 12:16:06: 2000000 INFO @ Wed, 08 Dec 2021 12:16:11: 7000000 INFO @ Wed, 08 Dec 2021 12:16:11: 11000000 INFO @ Wed, 08 Dec 2021 12:16:14: 3000000 INFO @ Wed, 08 Dec 2021 12:16:18: 8000000 INFO @ Wed, 08 Dec 2021 12:16:19: 12000000 INFO @ Wed, 08 Dec 2021 12:16:21: 4000000 INFO @ Wed, 08 Dec 2021 12:16:25: 9000000 INFO @ Wed, 08 Dec 2021 12:16:26: 13000000 INFO @ Wed, 08 Dec 2021 12:16:28: 5000000 INFO @ Wed, 08 Dec 2021 12:16:32: 10000000 INFO @ Wed, 08 Dec 2021 12:16:34: 14000000 INFO @ Wed, 08 Dec 2021 12:16:34: 6000000 INFO @ Wed, 08 Dec 2021 12:16:39: 11000000 INFO @ Wed, 08 Dec 2021 12:16:41: 15000000 INFO @ Wed, 08 Dec 2021 12:16:42: 7000000 INFO @ Wed, 08 Dec 2021 12:16:44: #1 tag size is determined as 75 bps INFO @ Wed, 08 Dec 2021 12:16:44: #1 tag size = 75 INFO @ Wed, 08 Dec 2021 12:16:44: #1 total tags in treatment: 15296909 INFO @ Wed, 08 Dec 2021 12:16:44: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 12:16:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 12:16:44: #1 tags after filtering in treatment: 15296909 INFO @ Wed, 08 Dec 2021 12:16:44: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 12:16:44: #1 finished! INFO @ Wed, 08 Dec 2021 12:16:44: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 12:16:44: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 12:16:45: #2 number of paired peaks: 290 WARNING @ Wed, 08 Dec 2021 12:16:45: Fewer paired peaks (290) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 290 pairs to build model! INFO @ Wed, 08 Dec 2021 12:16:45: start model_add_line... INFO @ Wed, 08 Dec 2021 12:16:45: start X-correlation... INFO @ Wed, 08 Dec 2021 12:16:45: end of X-cor INFO @ Wed, 08 Dec 2021 12:16:45: #2 finished! INFO @ Wed, 08 Dec 2021 12:16:45: #2 predicted fragment length is 48 bps INFO @ Wed, 08 Dec 2021 12:16:45: #2 alternative fragment length(s) may be 2,48 bps INFO @ Wed, 08 Dec 2021 12:16:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10569196/SRX10569196.05_model.r WARNING @ Wed, 08 Dec 2021 12:16:45: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 12:16:45: #2 You may need to consider one of the other alternative d(s): 2,48 WARNING @ Wed, 08 Dec 2021 12:16:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 12:16:45: #3 Call peaks... INFO @ Wed, 08 Dec 2021 12:16:45: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 12:16:46: 12000000 INFO @ Wed, 08 Dec 2021 12:16:49: 8000000 INFO @ Wed, 08 Dec 2021 12:16:53: 13000000 INFO @ Wed, 08 Dec 2021 12:16:56: 9000000 INFO @ Wed, 08 Dec 2021 12:17:00: 14000000 INFO @ Wed, 08 Dec 2021 12:17:03: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 12:17:07: 15000000 INFO @ Wed, 08 Dec 2021 12:17:09: #1 tag size is determined as 75 bps INFO @ Wed, 08 Dec 2021 12:17:09: #1 tag size = 75 INFO @ Wed, 08 Dec 2021 12:17:09: #1 total tags in treatment: 15296909 INFO @ Wed, 08 Dec 2021 12:17:09: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 12:17:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 12:17:09: #1 tags after filtering in treatment: 15296909 INFO @ Wed, 08 Dec 2021 12:17:09: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 12:17:09: #1 finished! INFO @ Wed, 08 Dec 2021 12:17:09: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 12:17:09: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 12:17:09: 11000000 INFO @ Wed, 08 Dec 2021 12:17:10: #2 number of paired peaks: 290 WARNING @ Wed, 08 Dec 2021 12:17:10: Fewer paired peaks (290) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 290 pairs to build model! INFO @ Wed, 08 Dec 2021 12:17:10: start model_add_line... INFO @ Wed, 08 Dec 2021 12:17:10: start X-correlation... INFO @ Wed, 08 Dec 2021 12:17:10: end of X-cor INFO @ Wed, 08 Dec 2021 12:17:10: #2 finished! INFO @ Wed, 08 Dec 2021 12:17:10: #2 predicted fragment length is 48 bps INFO @ Wed, 08 Dec 2021 12:17:10: #2 alternative fragment length(s) may be 2,48 bps INFO @ Wed, 08 Dec 2021 12:17:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10569196/SRX10569196.10_model.r WARNING @ Wed, 08 Dec 2021 12:17:10: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 12:17:10: #2 You may need to consider one of the other alternative d(s): 2,48 WARNING @ Wed, 08 Dec 2021 12:17:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 12:17:10: #3 Call peaks... INFO @ Wed, 08 Dec 2021 12:17:10: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 12:17:10: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 12:17:16: 12000000 INFO @ Wed, 08 Dec 2021 12:17:22: 13000000 INFO @ Wed, 08 Dec 2021 12:17:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10569196/SRX10569196.05_peaks.xls INFO @ Wed, 08 Dec 2021 12:17:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10569196/SRX10569196.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 12:17:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10569196/SRX10569196.05_summits.bed INFO @ Wed, 08 Dec 2021 12:17:23: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (666 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 12:17:29: 14000000 INFO @ Wed, 08 Dec 2021 12:17:35: 15000000 INFO @ Wed, 08 Dec 2021 12:17:36: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 12:17:37: #1 tag size is determined as 75 bps INFO @ Wed, 08 Dec 2021 12:17:37: #1 tag size = 75 INFO @ Wed, 08 Dec 2021 12:17:37: #1 total tags in treatment: 15296909 INFO @ Wed, 08 Dec 2021 12:17:37: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 12:17:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 12:17:38: #1 tags after filtering in treatment: 15296909 INFO @ Wed, 08 Dec 2021 12:17:38: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 08 Dec 2021 12:17:38: #1 finished! INFO @ Wed, 08 Dec 2021 12:17:38: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 12:17:38: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 12:17:39: #2 number of paired peaks: 290 WARNING @ Wed, 08 Dec 2021 12:17:39: Fewer paired peaks (290) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 290 pairs to build model! INFO @ Wed, 08 Dec 2021 12:17:39: start model_add_line... INFO @ Wed, 08 Dec 2021 12:17:39: start X-correlation... INFO @ Wed, 08 Dec 2021 12:17:39: end of X-cor INFO @ Wed, 08 Dec 2021 12:17:39: #2 finished! INFO @ Wed, 08 Dec 2021 12:17:39: #2 predicted fragment length is 48 bps INFO @ Wed, 08 Dec 2021 12:17:39: #2 alternative fragment length(s) may be 2,48 bps INFO @ Wed, 08 Dec 2021 12:17:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10569196/SRX10569196.20_model.r WARNING @ Wed, 08 Dec 2021 12:17:39: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 12:17:39: #2 You may need to consider one of the other alternative d(s): 2,48 WARNING @ Wed, 08 Dec 2021 12:17:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 12:17:39: #3 Call peaks... INFO @ Wed, 08 Dec 2021 12:17:39: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 12:17:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10569196/SRX10569196.10_peaks.xls INFO @ Wed, 08 Dec 2021 12:17:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10569196/SRX10569196.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 12:17:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10569196/SRX10569196.10_summits.bed INFO @ Wed, 08 Dec 2021 12:17:48: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (424 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 12:18:04: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 12:18:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10569196/SRX10569196.20_peaks.xls INFO @ Wed, 08 Dec 2021 12:18:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10569196/SRX10569196.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 12:18:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10569196/SRX10569196.20_summits.bed INFO @ Wed, 08 Dec 2021 12:18:16: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (166 records, 4 fields): 1 millis CompletedMACS2peakCalling