Job ID = 6453221 SRX = SRX1091592 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:09:03 prefetch.2.10.7: 1) Downloading 'SRR2096476'... 2020-06-21T08:09:03 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:13:28 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:13:28 prefetch.2.10.7: 1) 'SRR2096476' was downloaded successfully 2020-06-21T08:13:28 prefetch.2.10.7: 'SRR2096476' has 0 unresolved dependencies Read 9395688 spots for SRR2096476/SRR2096476.sra Written 9395688 spots for SRR2096476/SRR2096476.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: 00:05:35 9395688 reads; of these: 9395688 (100.00%) were unpaired; of these: 430192 (4.58%) aligned 0 times 8313261 (88.48%) aligned exactly 1 time 652235 (6.94%) aligned >1 times 95.42% overall alignment rate Time searching: 00:05:35 Overall time: 00:05:35 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 8 files... [bam_rmdupse_core] 3117804 / 8965496 = 0.3478 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 17:24:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1091592/SRX1091592.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1091592/SRX1091592.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1091592/SRX1091592.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1091592/SRX1091592.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 17:24:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:24:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:24:49: 1000000 INFO @ Sun, 21 Jun 2020 17:24:58: 2000000 INFO @ Sun, 21 Jun 2020 17:25:07: 3000000 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 17:25:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1091592/SRX1091592.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1091592/SRX1091592.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1091592/SRX1091592.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1091592/SRX1091592.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 17:25:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:25:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:25:17: 4000000 INFO @ Sun, 21 Jun 2020 17:25:22: 1000000 INFO @ Sun, 21 Jun 2020 17:25:28: 5000000 INFO @ Sun, 21 Jun 2020 17:25:32: 2000000 INFO @ Sun, 21 Jun 2020 17:25:37: #1 tag size is determined as 148 bps INFO @ Sun, 21 Jun 2020 17:25:37: #1 tag size = 148 INFO @ Sun, 21 Jun 2020 17:25:37: #1 total tags in treatment: 5847692 INFO @ Sun, 21 Jun 2020 17:25:37: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:25:37: #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 17:25:37: #1 tags after filtering in treatment: 5847365 INFO @ Sun, 21 Jun 2020 17:25:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:25:37: #1 finished! INFO @ Sun, 21 Jun 2020 17:25:37: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:25:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:25:37: #2 number of paired peaks: 3419 INFO @ Sun, 21 Jun 2020 17:25:37: start model_add_line... INFO @ Sun, 21 Jun 2020 17:25:37: start X-correlation... INFO @ Sun, 21 Jun 2020 17:25:38: end of X-cor INFO @ Sun, 21 Jun 2020 17:25:38: #2 finished! INFO @ Sun, 21 Jun 2020 17:25:38: #2 predicted fragment length is 169 bps INFO @ Sun, 21 Jun 2020 17:25:38: #2 alternative fragment length(s) may be 169 bps INFO @ Sun, 21 Jun 2020 17:25:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1091592/SRX1091592.05_model.r WARNING @ Sun, 21 Jun 2020 17:25:38: #2 Since the d (169) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:25:38: #2 You may need to consider one of the other alternative d(s): 169 WARNING @ Sun, 21 Jun 2020 17:25:38: #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 17:25:38: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:25:38: #3 Pre-compute pvalue-qvalue table... 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 17:25:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1091592/SRX1091592.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1091592/SRX1091592.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1091592/SRX1091592.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1091592/SRX1091592.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 17:25:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:25:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:25:42: 3000000 INFO @ Sun, 21 Jun 2020 17:25:51: 1000000 INFO @ Sun, 21 Jun 2020 17:25:52: 4000000 INFO @ Sun, 21 Jun 2020 17:25:54: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:26:01: 2000000 INFO @ Sun, 21 Jun 2020 17:26:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1091592/SRX1091592.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:26:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1091592/SRX1091592.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:26:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1091592/SRX1091592.05_summits.bed INFO @ Sun, 21 Jun 2020 17:26:03: Done! INFO @ Sun, 21 Jun 2020 17:26:03: 5000000 pass1 - making usageList (195 chroms): 2 millis pass2 - checking and writing primary data (10246 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:26:11: 3000000 INFO @ Sun, 21 Jun 2020 17:26:12: #1 tag size is determined as 148 bps INFO @ Sun, 21 Jun 2020 17:26:12: #1 tag size = 148 INFO @ Sun, 21 Jun 2020 17:26:12: #1 total tags in treatment: 5847692 INFO @ Sun, 21 Jun 2020 17:26:12: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:26:12: #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 17:26:12: #1 tags after filtering in treatment: 5847365 INFO @ Sun, 21 Jun 2020 17:26:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:26:12: #1 finished! INFO @ Sun, 21 Jun 2020 17:26:12: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:26:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:26:13: #2 number of paired peaks: 3419 INFO @ Sun, 21 Jun 2020 17:26:13: start model_add_line... INFO @ Sun, 21 Jun 2020 17:26:13: start X-correlation... INFO @ Sun, 21 Jun 2020 17:26:13: end of X-cor INFO @ Sun, 21 Jun 2020 17:26:13: #2 finished! INFO @ Sun, 21 Jun 2020 17:26:13: #2 predicted fragment length is 169 bps INFO @ Sun, 21 Jun 2020 17:26:13: #2 alternative fragment length(s) may be 169 bps INFO @ Sun, 21 Jun 2020 17:26:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1091592/SRX1091592.10_model.r WARNING @ Sun, 21 Jun 2020 17:26:13: #2 Since the d (169) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:26:13: #2 You may need to consider one of the other alternative d(s): 169 WARNING @ Sun, 21 Jun 2020 17:26:13: #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 17:26:13: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:26:13: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:26:20: 4000000 INFO @ Sun, 21 Jun 2020 17:26:29: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:26:30: 5000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:26:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1091592/SRX1091592.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:26:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1091592/SRX1091592.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:26:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1091592/SRX1091592.10_summits.bed INFO @ Sun, 21 Jun 2020 17:26:37: Done! pass1 - making usageList (123 chroms): 1 millis pass2 - checking and writing primary data (5324 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:26:38: #1 tag size is determined as 148 bps INFO @ Sun, 21 Jun 2020 17:26:38: #1 tag size = 148 INFO @ Sun, 21 Jun 2020 17:26:38: #1 total tags in treatment: 5847692 INFO @ Sun, 21 Jun 2020 17:26:38: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:26:38: #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 17:26:38: #1 tags after filtering in treatment: 5847365 INFO @ Sun, 21 Jun 2020 17:26:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:26:38: #1 finished! INFO @ Sun, 21 Jun 2020 17:26:38: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:26:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:26:39: #2 number of paired peaks: 3419 INFO @ Sun, 21 Jun 2020 17:26:39: start model_add_line... INFO @ Sun, 21 Jun 2020 17:26:39: start X-correlation... INFO @ Sun, 21 Jun 2020 17:26:39: end of X-cor INFO @ Sun, 21 Jun 2020 17:26:39: #2 finished! INFO @ Sun, 21 Jun 2020 17:26:39: #2 predicted fragment length is 169 bps INFO @ Sun, 21 Jun 2020 17:26:39: #2 alternative fragment length(s) may be 169 bps INFO @ Sun, 21 Jun 2020 17:26:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1091592/SRX1091592.20_model.r WARNING @ Sun, 21 Jun 2020 17:26:39: #2 Since the d (169) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:26:39: #2 You may need to consider one of the other alternative d(s): 169 WARNING @ Sun, 21 Jun 2020 17:26:39: #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 17:26:39: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:26:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:26:55: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:27:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1091592/SRX1091592.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:27:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1091592/SRX1091592.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:27:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1091592/SRX1091592.20_summits.bed INFO @ Sun, 21 Jun 2020 17:27:02: Done! pass1 - making usageList (71 chroms): 2 millis pass2 - checking and writing primary data (2519 records, 4 fields): 5 millis CompletedMACS2peakCalling