Job ID = 6455142 SRX = SRX2788643 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:42:26 prefetch.2.10.7: 1) Downloading 'SRR5515263'... 2020-06-21T09:42:26 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:49:13 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:49:13 prefetch.2.10.7: 1) 'SRR5515263' was downloaded successfully 2020-06-21T09:49:13 prefetch.2.10.7: 'SRR5515263' has 0 unresolved dependencies Read 25037552 spots for SRR5515263/SRR5515263.sra Written 25037552 spots for SRR5515263/SRR5515263.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: 00:10:07 25037552 reads; of these: 25037552 (100.00%) were unpaired; of these: 943215 (3.77%) aligned 0 times 19882028 (79.41%) aligned exactly 1 time 4212309 (16.82%) aligned >1 times 96.23% overall alignment rate Time searching: 00:10:07 Overall time: 00:10:07 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 11268735 / 24094337 = 0.4677 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 @ Sun, 21 Jun 2020 19:08:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2788643/SRX2788643.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2788643/SRX2788643.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2788643/SRX2788643.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2788643/SRX2788643.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 @ Sun, 21 Jun 2020 19:08:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:08:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:08:59: 1000000 INFO @ Sun, 21 Jun 2020 19:09:05: 2000000 INFO @ Sun, 21 Jun 2020 19:09:11: 3000000 INFO @ Sun, 21 Jun 2020 19:09:17: 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 @ Sun, 21 Jun 2020 19:09:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2788643/SRX2788643.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2788643/SRX2788643.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2788643/SRX2788643.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2788643/SRX2788643.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 @ Sun, 21 Jun 2020 19:09:23: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:09:23: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:09:23: 5000000 INFO @ Sun, 21 Jun 2020 19:09:29: 1000000 INFO @ Sun, 21 Jun 2020 19:09:29: 6000000 INFO @ Sun, 21 Jun 2020 19:09:36: 7000000 INFO @ Sun, 21 Jun 2020 19:09:36: 2000000 INFO @ Sun, 21 Jun 2020 19:09:42: 8000000 INFO @ Sun, 21 Jun 2020 19:09:43: 3000000 INFO @ Sun, 21 Jun 2020 19:09:49: 9000000 INFO @ Sun, 21 Jun 2020 19:09:49: 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 @ Sun, 21 Jun 2020 19:09:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2788643/SRX2788643.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2788643/SRX2788643.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2788643/SRX2788643.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2788643/SRX2788643.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 @ Sun, 21 Jun 2020 19:09:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:09:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:09:55: 10000000 INFO @ Sun, 21 Jun 2020 19:09:56: 5000000 INFO @ Sun, 21 Jun 2020 19:09:59: 1000000 INFO @ Sun, 21 Jun 2020 19:10:03: 6000000 INFO @ Sun, 21 Jun 2020 19:10:03: 11000000 INFO @ Sun, 21 Jun 2020 19:10:06: 2000000 INFO @ Sun, 21 Jun 2020 19:10:09: 7000000 INFO @ Sun, 21 Jun 2020 19:10:09: 12000000 INFO @ Sun, 21 Jun 2020 19:10:12: 3000000 INFO @ Sun, 21 Jun 2020 19:10:15: #1 tag size is determined as 100 bps INFO @ Sun, 21 Jun 2020 19:10:15: #1 tag size = 100 INFO @ Sun, 21 Jun 2020 19:10:15: #1 total tags in treatment: 12825602 INFO @ Sun, 21 Jun 2020 19:10:15: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:10:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:10:16: #1 tags after filtering in treatment: 12825458 INFO @ Sun, 21 Jun 2020 19:10:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:10:16: #1 finished! INFO @ Sun, 21 Jun 2020 19:10:16: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:10:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:10:16: 8000000 INFO @ Sun, 21 Jun 2020 19:10:17: #2 number of paired peaks: 2964 INFO @ Sun, 21 Jun 2020 19:10:17: start model_add_line... INFO @ Sun, 21 Jun 2020 19:10:17: start X-correlation... INFO @ Sun, 21 Jun 2020 19:10:17: end of X-cor INFO @ Sun, 21 Jun 2020 19:10:17: #2 finished! INFO @ Sun, 21 Jun 2020 19:10:17: #2 predicted fragment length is 147 bps INFO @ Sun, 21 Jun 2020 19:10:17: #2 alternative fragment length(s) may be 147 bps INFO @ Sun, 21 Jun 2020 19:10:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2788643/SRX2788643.05_model.r WARNING @ Sun, 21 Jun 2020 19:10:17: #2 Since the d (147) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:10:17: #2 You may need to consider one of the other alternative d(s): 147 WARNING @ Sun, 21 Jun 2020 19:10:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 19:10:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:10:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:10:19: 4000000 INFO @ Sun, 21 Jun 2020 19:10:23: 9000000 INFO @ Sun, 21 Jun 2020 19:10:25: 5000000 INFO @ Sun, 21 Jun 2020 19:10:29: 10000000 INFO @ Sun, 21 Jun 2020 19:10:32: 6000000 INFO @ Sun, 21 Jun 2020 19:10:36: 11000000 INFO @ Sun, 21 Jun 2020 19:10:38: 7000000 INFO @ Sun, 21 Jun 2020 19:10:43: 12000000 INFO @ Sun, 21 Jun 2020 19:10:45: 8000000 INFO @ Sun, 21 Jun 2020 19:10:49: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:10:49: #1 tag size is determined as 100 bps INFO @ Sun, 21 Jun 2020 19:10:49: #1 tag size = 100 INFO @ Sun, 21 Jun 2020 19:10:49: #1 total tags in treatment: 12825602 INFO @ Sun, 21 Jun 2020 19:10:49: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:10:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:10:49: #1 tags after filtering in treatment: 12825458 INFO @ Sun, 21 Jun 2020 19:10:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:10:49: #1 finished! INFO @ Sun, 21 Jun 2020 19:10:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:10:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:10:50: #2 number of paired peaks: 2964 INFO @ Sun, 21 Jun 2020 19:10:50: start model_add_line... INFO @ Sun, 21 Jun 2020 19:10:51: start X-correlation... INFO @ Sun, 21 Jun 2020 19:10:51: end of X-cor INFO @ Sun, 21 Jun 2020 19:10:51: #2 finished! INFO @ Sun, 21 Jun 2020 19:10:51: #2 predicted fragment length is 147 bps INFO @ Sun, 21 Jun 2020 19:10:51: #2 alternative fragment length(s) may be 147 bps INFO @ Sun, 21 Jun 2020 19:10:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2788643/SRX2788643.10_model.r WARNING @ Sun, 21 Jun 2020 19:10:51: #2 Since the d (147) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:10:51: #2 You may need to consider one of the other alternative d(s): 147 WARNING @ Sun, 21 Jun 2020 19:10:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 19:10:51: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:10:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:10:51: 9000000 INFO @ Sun, 21 Jun 2020 19:10:57: 10000000 INFO @ Sun, 21 Jun 2020 19:11:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2788643/SRX2788643.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:11:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2788643/SRX2788643.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:11:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2788643/SRX2788643.05_summits.bed INFO @ Sun, 21 Jun 2020 19:11:04: Done! INFO @ Sun, 21 Jun 2020 19:11:04: 11000000 pass1 - making usageList (315 chroms): 2 millis pass2 - checking and writing primary data (6233 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:11:10: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:11:16: #1 tag size is determined as 100 bps INFO @ Sun, 21 Jun 2020 19:11:16: #1 tag size = 100 INFO @ Sun, 21 Jun 2020 19:11:16: #1 total tags in treatment: 12825602 INFO @ Sun, 21 Jun 2020 19:11:16: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:11:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:11:16: #1 tags after filtering in treatment: 12825458 INFO @ Sun, 21 Jun 2020 19:11:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:11:16: #1 finished! INFO @ Sun, 21 Jun 2020 19:11:16: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:11:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:11:17: #2 number of paired peaks: 2964 INFO @ Sun, 21 Jun 2020 19:11:17: start model_add_line... INFO @ Sun, 21 Jun 2020 19:11:17: start X-correlation... INFO @ Sun, 21 Jun 2020 19:11:17: end of X-cor INFO @ Sun, 21 Jun 2020 19:11:17: #2 finished! INFO @ Sun, 21 Jun 2020 19:11:17: #2 predicted fragment length is 147 bps INFO @ Sun, 21 Jun 2020 19:11:17: #2 alternative fragment length(s) may be 147 bps INFO @ Sun, 21 Jun 2020 19:11:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2788643/SRX2788643.20_model.r WARNING @ Sun, 21 Jun 2020 19:11:17: #2 Since the d (147) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:11:17: #2 You may need to consider one of the other alternative d(s): 147 WARNING @ Sun, 21 Jun 2020 19:11:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 19:11:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:11:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:11:22: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:11:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2788643/SRX2788643.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:11:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2788643/SRX2788643.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:11:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2788643/SRX2788643.10_summits.bed INFO @ Sun, 21 Jun 2020 19:11:38: Done! pass1 - making usageList (221 chroms): 1 millis pass2 - checking and writing primary data (4669 records, 4 fields): 51 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:11:49: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:12:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2788643/SRX2788643.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:12:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2788643/SRX2788643.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:12:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2788643/SRX2788643.20_summits.bed INFO @ Sun, 21 Jun 2020 19:12:04: Done! pass1 - making usageList (140 chroms): 2 millis pass2 - checking and writing primary data (3133 records, 4 fields): 8 millis CompletedMACS2peakCalling