Job ID = 6498759 SRX = SRX750082 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T00:03:10 prefetch.2.10.7: 1) Downloading 'SRR1638776'... 2020-06-26T00:03:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T00:08:36 prefetch.2.10.7: HTTPS download succeed 2020-06-26T00:08:36 prefetch.2.10.7: 1) 'SRR1638776' was downloaded successfully Read 43126269 spots for SRR1638776/SRR1638776.sra Written 43126269 spots for SRR1638776/SRR1638776.sra 2020-06-26T00:11:00 prefetch.2.10.7: 1) Downloading 'SRR1638777'... 2020-06-26T00:11:00 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T00:15:12 prefetch.2.10.7: HTTPS download succeed 2020-06-26T00:15:12 prefetch.2.10.7: 1) 'SRR1638777' was downloaded successfully Read 40323482 spots for SRR1638777/SRR1638777.sra Written 40323482 spots for SRR1638777/SRR1638777.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: 00:40:13 83449751 reads; of these: 83449751 (100.00%) were unpaired; of these: 6625868 (7.94%) aligned 0 times 44092957 (52.84%) aligned exactly 1 time 32730926 (39.22%) aligned >1 times 92.06% overall alignment rate Time searching: 00:40:13 Overall time: 00:40:13 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 32 files... [bam_rmdupse_core] 68879178 / 76823883 = 0.8966 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 10:12:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX750082/SRX750082.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX750082/SRX750082.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX750082/SRX750082.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX750082/SRX750082.bam'] # control file = None # effective genome size = 1.20e+08 # 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 10:12:03: #1 read tag files... INFO @ Fri, 26 Jun 2020 10:12:03: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 10:12:09: 1000000 INFO @ Fri, 26 Jun 2020 10:12:15: 2000000 INFO @ Fri, 26 Jun 2020 10:12:20: 3000000 INFO @ Fri, 26 Jun 2020 10:12:26: 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 10:12:32: 5000000 INFO @ Fri, 26 Jun 2020 10:12:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX750082/SRX750082.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX750082/SRX750082.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX750082/SRX750082.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX750082/SRX750082.bam'] # control file = None # effective genome size = 1.20e+08 # 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 10:12:33: #1 read tag files... INFO @ Fri, 26 Jun 2020 10:12:33: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 10:12:37: 6000000 INFO @ Fri, 26 Jun 2020 10:12:40: 1000000 INFO @ Fri, 26 Jun 2020 10:12:43: 7000000 INFO @ Fri, 26 Jun 2020 10:12:46: 2000000 INFO @ Fri, 26 Jun 2020 10:12:49: #1 tag size is determined as 67 bps INFO @ Fri, 26 Jun 2020 10:12:49: #1 tag size = 67 INFO @ Fri, 26 Jun 2020 10:12:49: #1 total tags in treatment: 7944705 INFO @ Fri, 26 Jun 2020 10:12:49: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 10:12:49: #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 10:12:49: #1 tags after filtering in treatment: 7944705 INFO @ Fri, 26 Jun 2020 10:12:49: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 10:12:49: #1 finished! INFO @ Fri, 26 Jun 2020 10:12:49: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 10:12:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 10:12:50: #2 number of paired peaks: 4151 INFO @ Fri, 26 Jun 2020 10:12:50: start model_add_line... INFO @ Fri, 26 Jun 2020 10:12:50: start X-correlation... INFO @ Fri, 26 Jun 2020 10:12:50: end of X-cor INFO @ Fri, 26 Jun 2020 10:12:50: #2 finished! INFO @ Fri, 26 Jun 2020 10:12:50: #2 predicted fragment length is 100 bps INFO @ Fri, 26 Jun 2020 10:12:50: #2 alternative fragment length(s) may be 100 bps INFO @ Fri, 26 Jun 2020 10:12:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX750082/SRX750082.05_model.r WARNING @ Fri, 26 Jun 2020 10:12:50: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 10:12:50: #2 You may need to consider one of the other alternative d(s): 100 WARNING @ Fri, 26 Jun 2020 10:12:50: #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 10:12:50: #3 Call peaks... INFO @ Fri, 26 Jun 2020 10:12:50: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 10:12:52: 3000000 INFO @ Fri, 26 Jun 2020 10:12:58: 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 10:13:03: 5000000 INFO @ Fri, 26 Jun 2020 10:13:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX750082/SRX750082.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX750082/SRX750082.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX750082/SRX750082.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX750082/SRX750082.bam'] # control file = None # effective genome size = 1.20e+08 # 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 10:13:04: #1 read tag files... INFO @ Fri, 26 Jun 2020 10:13:04: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 10:13:09: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 10:13:09: 6000000 INFO @ Fri, 26 Jun 2020 10:13:10: 1000000 INFO @ Fri, 26 Jun 2020 10:13:16: 7000000 INFO @ Fri, 26 Jun 2020 10:13:17: 2000000 INFO @ Fri, 26 Jun 2020 10:13:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX750082/SRX750082.05_peaks.xls INFO @ Fri, 26 Jun 2020 10:13:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX750082/SRX750082.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 10:13:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX750082/SRX750082.05_summits.bed INFO @ Fri, 26 Jun 2020 10:13:19: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9721 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 10:13:21: #1 tag size is determined as 67 bps INFO @ Fri, 26 Jun 2020 10:13:21: #1 tag size = 67 INFO @ Fri, 26 Jun 2020 10:13:21: #1 total tags in treatment: 7944705 INFO @ Fri, 26 Jun 2020 10:13:21: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 10:13:21: #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 10:13:22: #1 tags after filtering in treatment: 7944705 INFO @ Fri, 26 Jun 2020 10:13:22: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 10:13:22: #1 finished! INFO @ Fri, 26 Jun 2020 10:13:22: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 10:13:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 10:13:22: #2 number of paired peaks: 4151 INFO @ Fri, 26 Jun 2020 10:13:22: start model_add_line... INFO @ Fri, 26 Jun 2020 10:13:22: start X-correlation... INFO @ Fri, 26 Jun 2020 10:13:22: end of X-cor INFO @ Fri, 26 Jun 2020 10:13:22: #2 finished! INFO @ Fri, 26 Jun 2020 10:13:22: #2 predicted fragment length is 100 bps INFO @ Fri, 26 Jun 2020 10:13:22: #2 alternative fragment length(s) may be 100 bps INFO @ Fri, 26 Jun 2020 10:13:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX750082/SRX750082.10_model.r WARNING @ Fri, 26 Jun 2020 10:13:22: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 10:13:22: #2 You may need to consider one of the other alternative d(s): 100 WARNING @ Fri, 26 Jun 2020 10:13:22: #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 10:13:22: #3 Call peaks... INFO @ Fri, 26 Jun 2020 10:13:22: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 10:13:23: 3000000 INFO @ Fri, 26 Jun 2020 10:13:30: 4000000 INFO @ Fri, 26 Jun 2020 10:13:36: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 10:13:41: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 10:13:42: 6000000 INFO @ Fri, 26 Jun 2020 10:13:48: 7000000 INFO @ Fri, 26 Jun 2020 10:13:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX750082/SRX750082.10_peaks.xls INFO @ Fri, 26 Jun 2020 10:13:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX750082/SRX750082.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 10:13:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX750082/SRX750082.10_summits.bed INFO @ Fri, 26 Jun 2020 10:13:50: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6416 records, 4 fields): 14 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 10:13:54: #1 tag size is determined as 67 bps INFO @ Fri, 26 Jun 2020 10:13:54: #1 tag size = 67 INFO @ Fri, 26 Jun 2020 10:13:54: #1 total tags in treatment: 7944705 INFO @ Fri, 26 Jun 2020 10:13:54: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 10:13:54: #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 10:13:55: #1 tags after filtering in treatment: 7944705 INFO @ Fri, 26 Jun 2020 10:13:55: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 10:13:55: #1 finished! INFO @ Fri, 26 Jun 2020 10:13:55: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 10:13:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 10:13:55: #2 number of paired peaks: 4151 INFO @ Fri, 26 Jun 2020 10:13:55: start model_add_line... INFO @ Fri, 26 Jun 2020 10:13:55: start X-correlation... INFO @ Fri, 26 Jun 2020 10:13:55: end of X-cor INFO @ Fri, 26 Jun 2020 10:13:55: #2 finished! INFO @ Fri, 26 Jun 2020 10:13:55: #2 predicted fragment length is 100 bps INFO @ Fri, 26 Jun 2020 10:13:55: #2 alternative fragment length(s) may be 100 bps INFO @ Fri, 26 Jun 2020 10:13:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX750082/SRX750082.20_model.r WARNING @ Fri, 26 Jun 2020 10:13:55: #2 Since the d (100) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 10:13:55: #2 You may need to consider one of the other alternative d(s): 100 WARNING @ Fri, 26 Jun 2020 10:13:55: #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 10:13:55: #3 Call peaks... INFO @ Fri, 26 Jun 2020 10:13:55: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 10:14:14: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 10:14:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX750082/SRX750082.20_peaks.xls INFO @ Fri, 26 Jun 2020 10:14:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX750082/SRX750082.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 10:14:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX750082/SRX750082.20_summits.bed INFO @ Fri, 26 Jun 2020 10:14:23: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4105 records, 4 fields): 5 millis CompletedMACS2peakCalling