Job ID = 6453473 SRX = SRX1167417 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:34:09 prefetch.2.10.7: 1) Downloading 'SRR2192441'... 2020-06-21T08:34:09 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:41:14 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:41:14 prefetch.2.10.7: 1) 'SRR2192441' was downloaded successfully Read 41046866 spots for SRR2192441/SRR2192441.sra Written 41046866 spots for SRR2192441/SRR2192441.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: 00:15:17 41046866 reads; of these: 41046866 (100.00%) were unpaired; of these: 1366206 (3.33%) aligned 0 times 12983301 (31.63%) aligned exactly 1 time 26697359 (65.04%) aligned >1 times 96.67% overall alignment rate Time searching: 00:15:17 Overall time: 00:15:17 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 20 files... [bam_rmdupse_core] 13309533 / 39680660 = 0.3354 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 18:10:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1167417/SRX1167417.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1167417/SRX1167417.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1167417/SRX1167417.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1167417/SRX1167417.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 18:10:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:10:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:10:44: 1000000 INFO @ Sun, 21 Jun 2020 18:10:50: 2000000 INFO @ Sun, 21 Jun 2020 18:10:56: 3000000 INFO @ Sun, 21 Jun 2020 18:11:02: 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 18:11:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1167417/SRX1167417.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1167417/SRX1167417.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1167417/SRX1167417.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1167417/SRX1167417.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 18:11:08: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:11:08: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:11:08: 5000000 INFO @ Sun, 21 Jun 2020 18:11:14: 6000000 INFO @ Sun, 21 Jun 2020 18:11:15: 1000000 INFO @ Sun, 21 Jun 2020 18:11:21: 7000000 INFO @ Sun, 21 Jun 2020 18:11:22: 2000000 INFO @ Sun, 21 Jun 2020 18:11:27: 8000000 INFO @ Sun, 21 Jun 2020 18:11:29: 3000000 INFO @ Sun, 21 Jun 2020 18:11:33: 9000000 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 18:11:36: 4000000 INFO @ Sun, 21 Jun 2020 18:11:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1167417/SRX1167417.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1167417/SRX1167417.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1167417/SRX1167417.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1167417/SRX1167417.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 18:11:38: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:11:38: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:11:39: 10000000 INFO @ Sun, 21 Jun 2020 18:11:43: 5000000 INFO @ Sun, 21 Jun 2020 18:11:45: 1000000 INFO @ Sun, 21 Jun 2020 18:11:46: 11000000 INFO @ Sun, 21 Jun 2020 18:11:51: 6000000 INFO @ Sun, 21 Jun 2020 18:11:52: 12000000 INFO @ Sun, 21 Jun 2020 18:11:52: 2000000 INFO @ Sun, 21 Jun 2020 18:11:58: 7000000 INFO @ Sun, 21 Jun 2020 18:11:58: 13000000 INFO @ Sun, 21 Jun 2020 18:12:00: 3000000 INFO @ Sun, 21 Jun 2020 18:12:04: 14000000 INFO @ Sun, 21 Jun 2020 18:12:05: 8000000 INFO @ Sun, 21 Jun 2020 18:12:07: 4000000 INFO @ Sun, 21 Jun 2020 18:12:10: 15000000 INFO @ Sun, 21 Jun 2020 18:12:12: 9000000 INFO @ Sun, 21 Jun 2020 18:12:14: 5000000 INFO @ Sun, 21 Jun 2020 18:12:16: 16000000 INFO @ Sun, 21 Jun 2020 18:12:20: 10000000 INFO @ Sun, 21 Jun 2020 18:12:21: 6000000 INFO @ Sun, 21 Jun 2020 18:12:23: 17000000 INFO @ Sun, 21 Jun 2020 18:12:27: 11000000 INFO @ Sun, 21 Jun 2020 18:12:28: 7000000 INFO @ Sun, 21 Jun 2020 18:12:29: 18000000 INFO @ Sun, 21 Jun 2020 18:12:34: 12000000 INFO @ Sun, 21 Jun 2020 18:12:35: 19000000 INFO @ Sun, 21 Jun 2020 18:12:35: 8000000 INFO @ Sun, 21 Jun 2020 18:12:41: 13000000 INFO @ Sun, 21 Jun 2020 18:12:42: 20000000 INFO @ Sun, 21 Jun 2020 18:12:43: 9000000 INFO @ Sun, 21 Jun 2020 18:12:48: 21000000 INFO @ Sun, 21 Jun 2020 18:12:49: 14000000 INFO @ Sun, 21 Jun 2020 18:12:50: 10000000 INFO @ Sun, 21 Jun 2020 18:12:55: 22000000 INFO @ Sun, 21 Jun 2020 18:12:56: 15000000 INFO @ Sun, 21 Jun 2020 18:12:58: 11000000 INFO @ Sun, 21 Jun 2020 18:13:01: 23000000 INFO @ Sun, 21 Jun 2020 18:13:03: 16000000 INFO @ Sun, 21 Jun 2020 18:13:05: 12000000 INFO @ Sun, 21 Jun 2020 18:13:08: 24000000 INFO @ Sun, 21 Jun 2020 18:13:11: 17000000 INFO @ Sun, 21 Jun 2020 18:13:12: 13000000 INFO @ Sun, 21 Jun 2020 18:13:14: 25000000 INFO @ Sun, 21 Jun 2020 18:13:18: 18000000 INFO @ Sun, 21 Jun 2020 18:13:19: 14000000 INFO @ Sun, 21 Jun 2020 18:13:20: 26000000 INFO @ Sun, 21 Jun 2020 18:13:23: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:13:23: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:13:23: #1 total tags in treatment: 26371127 INFO @ Sun, 21 Jun 2020 18:13:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:13:23: #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 18:13:24: #1 tags after filtering in treatment: 26371127 INFO @ Sun, 21 Jun 2020 18:13:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:13:24: #1 finished! INFO @ Sun, 21 Jun 2020 18:13:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:13:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:13:26: #2 number of paired peaks: 2045 INFO @ Sun, 21 Jun 2020 18:13:26: start model_add_line... INFO @ Sun, 21 Jun 2020 18:13:26: start X-correlation... INFO @ Sun, 21 Jun 2020 18:13:26: end of X-cor INFO @ Sun, 21 Jun 2020 18:13:26: #2 finished! INFO @ Sun, 21 Jun 2020 18:13:26: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 18:13:26: #2 alternative fragment length(s) may be 1,30 bps INFO @ Sun, 21 Jun 2020 18:13:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1167417/SRX1167417.05_model.r WARNING @ Sun, 21 Jun 2020 18:13:26: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:13:26: #2 You may need to consider one of the other alternative d(s): 1,30 WARNING @ Sun, 21 Jun 2020 18:13:26: #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 18:13:26: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:13:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:13:27: 19000000 INFO @ Sun, 21 Jun 2020 18:13:27: 15000000 INFO @ Sun, 21 Jun 2020 18:13:35: 16000000 INFO @ Sun, 21 Jun 2020 18:13:35: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:13:42: 17000000 INFO @ Sun, 21 Jun 2020 18:13:43: 21000000 INFO @ Sun, 21 Jun 2020 18:13:50: 18000000 INFO @ Sun, 21 Jun 2020 18:13:50: 22000000 INFO @ Sun, 21 Jun 2020 18:13:58: 23000000 INFO @ Sun, 21 Jun 2020 18:13:58: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:13:59: 19000000 INFO @ Sun, 21 Jun 2020 18:14:06: 24000000 INFO @ Sun, 21 Jun 2020 18:14:07: 20000000 INFO @ Sun, 21 Jun 2020 18:14:14: 25000000 INFO @ Sun, 21 Jun 2020 18:14:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1167417/SRX1167417.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:14:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1167417/SRX1167417.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:14:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1167417/SRX1167417.05_summits.bed INFO @ Sun, 21 Jun 2020 18:14:14: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:14:14: 21000000 INFO @ Sun, 21 Jun 2020 18:14:21: 26000000 INFO @ Sun, 21 Jun 2020 18:14:22: 22000000 INFO @ Sun, 21 Jun 2020 18:14:24: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:14:24: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:14:24: #1 total tags in treatment: 26371127 INFO @ Sun, 21 Jun 2020 18:14:24: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:14:24: #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 18:14:25: #1 tags after filtering in treatment: 26371127 INFO @ Sun, 21 Jun 2020 18:14:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:14:25: #1 finished! INFO @ Sun, 21 Jun 2020 18:14:25: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:14:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:14:27: #2 number of paired peaks: 2045 INFO @ Sun, 21 Jun 2020 18:14:27: start model_add_line... INFO @ Sun, 21 Jun 2020 18:14:27: start X-correlation... INFO @ Sun, 21 Jun 2020 18:14:27: end of X-cor INFO @ Sun, 21 Jun 2020 18:14:27: #2 finished! INFO @ Sun, 21 Jun 2020 18:14:27: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 18:14:27: #2 alternative fragment length(s) may be 1,30 bps INFO @ Sun, 21 Jun 2020 18:14:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1167417/SRX1167417.10_model.r WARNING @ Sun, 21 Jun 2020 18:14:27: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:14:27: #2 You may need to consider one of the other alternative d(s): 1,30 WARNING @ Sun, 21 Jun 2020 18:14:27: #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 18:14:27: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:14:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:14:29: 23000000 INFO @ Sun, 21 Jun 2020 18:14:37: 24000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:14:43: 25000000 INFO @ Sun, 21 Jun 2020 18:14:49: 26000000 INFO @ Sun, 21 Jun 2020 18:14:52: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:14:52: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:14:52: #1 total tags in treatment: 26371127 INFO @ Sun, 21 Jun 2020 18:14:52: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:14:52: #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 18:14:53: #1 tags after filtering in treatment: 26371127 INFO @ Sun, 21 Jun 2020 18:14:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:14:53: #1 finished! INFO @ Sun, 21 Jun 2020 18:14:53: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:14:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:14:54: #2 number of paired peaks: 2045 INFO @ Sun, 21 Jun 2020 18:14:54: start model_add_line... INFO @ Sun, 21 Jun 2020 18:14:55: start X-correlation... INFO @ Sun, 21 Jun 2020 18:14:55: end of X-cor INFO @ Sun, 21 Jun 2020 18:14:55: #2 finished! INFO @ Sun, 21 Jun 2020 18:14:55: #2 predicted fragment length is 1 bps INFO @ Sun, 21 Jun 2020 18:14:55: #2 alternative fragment length(s) may be 1,30 bps INFO @ Sun, 21 Jun 2020 18:14:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1167417/SRX1167417.20_model.r WARNING @ Sun, 21 Jun 2020 18:14:55: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:14:55: #2 You may need to consider one of the other alternative d(s): 1,30 WARNING @ Sun, 21 Jun 2020 18:14:55: #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 18:14:55: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:14:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:15:00: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:15:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1167417/SRX1167417.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:15:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1167417/SRX1167417.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:15:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1167417/SRX1167417.10_summits.bed INFO @ Sun, 21 Jun 2020 18:15:16: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:15:28: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:15:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1167417/SRX1167417.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:15:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1167417/SRX1167417.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:15:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1167417/SRX1167417.20_summits.bed INFO @ Sun, 21 Jun 2020 18:15:44: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling