Job ID = 6458621 SRX = SRX5343152 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:32:52 prefetch.2.10.7: 1) Downloading 'SRR8540852'... 2020-06-21T12:32:52 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:35:20 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:35:20 prefetch.2.10.7: 1) 'SRR8540852' was downloaded successfully 2020-06-21T12:35:20 prefetch.2.10.7: 'SRR8540852' has 0 unresolved dependencies Read 28267185 spots for SRR8540852/SRR8540852.sra Written 28267185 spots for SRR8540852/SRR8540852.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:15 28267185 reads; of these: 28267185 (100.00%) were unpaired; of these: 5203077 (18.41%) aligned 0 times 16853755 (59.62%) aligned exactly 1 time 6210353 (21.97%) aligned >1 times 81.59% overall alignment rate Time searching: 00:08:16 Overall time: 00:08:16 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] 11750315 / 23064108 = 0.5095 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 21:49:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343152/SRX5343152.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343152/SRX5343152.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343152/SRX5343152.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343152/SRX5343152.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 21:49:48: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:49:48: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:49:55: 1000000 INFO @ Sun, 21 Jun 2020 21:50:02: 2000000 INFO @ Sun, 21 Jun 2020 21:50:08: 3000000 INFO @ Sun, 21 Jun 2020 21:50:15: 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 21:50:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343152/SRX5343152.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343152/SRX5343152.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343152/SRX5343152.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343152/SRX5343152.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 21:50:18: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:50:18: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:50:22: 5000000 INFO @ Sun, 21 Jun 2020 21:50:24: 1000000 INFO @ Sun, 21 Jun 2020 21:50:30: 6000000 INFO @ Sun, 21 Jun 2020 21:50:31: 2000000 INFO @ Sun, 21 Jun 2020 21:50:37: 7000000 INFO @ Sun, 21 Jun 2020 21:50:38: 3000000 INFO @ Sun, 21 Jun 2020 21:50:44: 8000000 INFO @ Sun, 21 Jun 2020 21:50:44: 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 21:50:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343152/SRX5343152.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343152/SRX5343152.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343152/SRX5343152.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343152/SRX5343152.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 21:50:49: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:50:49: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:50:51: 5000000 INFO @ Sun, 21 Jun 2020 21:50:51: 9000000 INFO @ Sun, 21 Jun 2020 21:50:56: 1000000 INFO @ Sun, 21 Jun 2020 21:50:57: 6000000 INFO @ Sun, 21 Jun 2020 21:50:59: 10000000 INFO @ Sun, 21 Jun 2020 21:51:04: 2000000 INFO @ Sun, 21 Jun 2020 21:51:04: 7000000 INFO @ Sun, 21 Jun 2020 21:51:06: 11000000 INFO @ Sun, 21 Jun 2020 21:51:08: #1 tag size is determined as 65 bps INFO @ Sun, 21 Jun 2020 21:51:08: #1 tag size = 65 INFO @ Sun, 21 Jun 2020 21:51:08: #1 total tags in treatment: 11313793 INFO @ Sun, 21 Jun 2020 21:51:08: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:51:08: #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 21:51:09: #1 tags after filtering in treatment: 11313791 INFO @ Sun, 21 Jun 2020 21:51:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:51:09: #1 finished! INFO @ Sun, 21 Jun 2020 21:51:09: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:51:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:51:10: #2 number of paired peaks: 1311 INFO @ Sun, 21 Jun 2020 21:51:10: start model_add_line... INFO @ Sun, 21 Jun 2020 21:51:10: start X-correlation... INFO @ Sun, 21 Jun 2020 21:51:10: end of X-cor INFO @ Sun, 21 Jun 2020 21:51:10: #2 finished! INFO @ Sun, 21 Jun 2020 21:51:10: #2 predicted fragment length is 88 bps INFO @ Sun, 21 Jun 2020 21:51:10: #2 alternative fragment length(s) may be 4,88,585,598 bps INFO @ Sun, 21 Jun 2020 21:51:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343152/SRX5343152.05_model.r WARNING @ Sun, 21 Jun 2020 21:51:10: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:51:10: #2 You may need to consider one of the other alternative d(s): 4,88,585,598 WARNING @ Sun, 21 Jun 2020 21:51:10: #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 21:51:10: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:51:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:51:10: 8000000 INFO @ Sun, 21 Jun 2020 21:51:11: 3000000 INFO @ Sun, 21 Jun 2020 21:51:17: 9000000 INFO @ Sun, 21 Jun 2020 21:51:18: 4000000 INFO @ Sun, 21 Jun 2020 21:51:24: 10000000 INFO @ Sun, 21 Jun 2020 21:51:25: 5000000 INFO @ Sun, 21 Jun 2020 21:51:31: 11000000 INFO @ Sun, 21 Jun 2020 21:51:32: 6000000 INFO @ Sun, 21 Jun 2020 21:51:33: #1 tag size is determined as 65 bps INFO @ Sun, 21 Jun 2020 21:51:33: #1 tag size = 65 INFO @ Sun, 21 Jun 2020 21:51:33: #1 total tags in treatment: 11313793 INFO @ Sun, 21 Jun 2020 21:51:33: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:51:33: #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 21:51:33: #1 tags after filtering in treatment: 11313791 INFO @ Sun, 21 Jun 2020 21:51:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:51:33: #1 finished! INFO @ Sun, 21 Jun 2020 21:51:33: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:51:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:51:33: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:51:34: #2 number of paired peaks: 1311 INFO @ Sun, 21 Jun 2020 21:51:34: start model_add_line... INFO @ Sun, 21 Jun 2020 21:51:34: start X-correlation... INFO @ Sun, 21 Jun 2020 21:51:34: end of X-cor INFO @ Sun, 21 Jun 2020 21:51:34: #2 finished! INFO @ Sun, 21 Jun 2020 21:51:34: #2 predicted fragment length is 88 bps INFO @ Sun, 21 Jun 2020 21:51:34: #2 alternative fragment length(s) may be 4,88,585,598 bps INFO @ Sun, 21 Jun 2020 21:51:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343152/SRX5343152.10_model.r WARNING @ Sun, 21 Jun 2020 21:51:34: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:51:34: #2 You may need to consider one of the other alternative d(s): 4,88,585,598 WARNING @ Sun, 21 Jun 2020 21:51:34: #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 21:51:34: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:51:34: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:51:39: 7000000 INFO @ Sun, 21 Jun 2020 21:51:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343152/SRX5343152.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:51:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343152/SRX5343152.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:51:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343152/SRX5343152.05_summits.bed INFO @ Sun, 21 Jun 2020 21:51:45: Done! pass1 - making usageList (829 chroms): 1 millis pass2 - checking and writing primary data (3022 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:51:45: 8000000 INFO @ Sun, 21 Jun 2020 21:51:52: 9000000 INFO @ Sun, 21 Jun 2020 21:51:56: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:51:59: 10000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:52:06: 11000000 INFO @ Sun, 21 Jun 2020 21:52:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343152/SRX5343152.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:52:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343152/SRX5343152.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:52:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343152/SRX5343152.10_summits.bed INFO @ Sun, 21 Jun 2020 21:52:07: Done! pass1 - making usageList (497 chroms): 1 millis pass2 - checking and writing primary data (1219 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:52:08: #1 tag size is determined as 65 bps INFO @ Sun, 21 Jun 2020 21:52:08: #1 tag size = 65 INFO @ Sun, 21 Jun 2020 21:52:08: #1 total tags in treatment: 11313793 INFO @ Sun, 21 Jun 2020 21:52:08: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:52:08: #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 21:52:09: #1 tags after filtering in treatment: 11313791 INFO @ Sun, 21 Jun 2020 21:52:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:52:09: #1 finished! INFO @ Sun, 21 Jun 2020 21:52:09: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:52:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:52:09: #2 number of paired peaks: 1311 INFO @ Sun, 21 Jun 2020 21:52:09: start model_add_line... INFO @ Sun, 21 Jun 2020 21:52:09: start X-correlation... INFO @ Sun, 21 Jun 2020 21:52:09: end of X-cor INFO @ Sun, 21 Jun 2020 21:52:09: #2 finished! INFO @ Sun, 21 Jun 2020 21:52:09: #2 predicted fragment length is 88 bps INFO @ Sun, 21 Jun 2020 21:52:09: #2 alternative fragment length(s) may be 4,88,585,598 bps INFO @ Sun, 21 Jun 2020 21:52:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343152/SRX5343152.20_model.r WARNING @ Sun, 21 Jun 2020 21:52:09: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:52:09: #2 You may need to consider one of the other alternative d(s): 4,88,585,598 WARNING @ Sun, 21 Jun 2020 21:52:09: #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 21:52:09: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:52:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:52:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:52:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343152/SRX5343152.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:52:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343152/SRX5343152.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:52:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343152/SRX5343152.20_summits.bed INFO @ Sun, 21 Jun 2020 21:52:43: Done! pass1 - making usageList (250 chroms): 1 millis pass2 - checking and writing primary data (462 records, 4 fields): 7 millis CompletedMACS2peakCalling