Job ID = 6455424 SRX = SRX287778 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:58:40 prefetch.2.10.7: 1) Downloading 'SRR869967'... 2020-06-21T09:58:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:01:43 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:01:43 prefetch.2.10.7: 1) 'SRR869967' was downloaded successfully Read 21014950 spots for SRR869967/SRR869967.sra Written 21014950 spots for SRR869967/SRR869967.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: 00:05:48 21014950 reads; of these: 21014950 (100.00%) were unpaired; of these: 1319320 (6.28%) aligned 0 times 15033855 (71.54%) aligned exactly 1 time 4661775 (22.18%) aligned >1 times 93.72% overall alignment rate Time searching: 00:05:48 Overall time: 00:05:48 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] 3193808 / 19695630 = 0.1622 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 19:13:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287778/SRX287778.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287778/SRX287778.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287778/SRX287778.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287778/SRX287778.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 19:13:42: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:13:42: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:13:48: 1000000 INFO @ Sun, 21 Jun 2020 19:13:54: 2000000 INFO @ Sun, 21 Jun 2020 19:14:00: 3000000 INFO @ Sun, 21 Jun 2020 19:14:06: 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 19:14:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287778/SRX287778.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287778/SRX287778.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287778/SRX287778.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287778/SRX287778.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 19:14:12: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:14:12: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:14:12: 5000000 INFO @ Sun, 21 Jun 2020 19:14:19: 6000000 INFO @ Sun, 21 Jun 2020 19:14:19: 1000000 INFO @ Sun, 21 Jun 2020 19:14:26: 7000000 INFO @ Sun, 21 Jun 2020 19:14:26: 2000000 INFO @ Sun, 21 Jun 2020 19:14:32: 8000000 INFO @ Sun, 21 Jun 2020 19:14:33: 3000000 INFO @ Sun, 21 Jun 2020 19:14:39: 9000000 INFO @ Sun, 21 Jun 2020 19:14:40: 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 19:14:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287778/SRX287778.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287778/SRX287778.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287778/SRX287778.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287778/SRX287778.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 19:14:42: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:14:42: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:14:46: 10000000 INFO @ Sun, 21 Jun 2020 19:14:47: 5000000 INFO @ Sun, 21 Jun 2020 19:14:49: 1000000 INFO @ Sun, 21 Jun 2020 19:14:54: 11000000 INFO @ Sun, 21 Jun 2020 19:14:54: 6000000 INFO @ Sun, 21 Jun 2020 19:14:57: 2000000 INFO @ Sun, 21 Jun 2020 19:15:01: 12000000 INFO @ Sun, 21 Jun 2020 19:15:01: 7000000 INFO @ Sun, 21 Jun 2020 19:15:04: 3000000 INFO @ Sun, 21 Jun 2020 19:15:08: 13000000 INFO @ Sun, 21 Jun 2020 19:15:08: 8000000 INFO @ Sun, 21 Jun 2020 19:15:11: 4000000 INFO @ Sun, 21 Jun 2020 19:15:15: 9000000 INFO @ Sun, 21 Jun 2020 19:15:16: 14000000 INFO @ Sun, 21 Jun 2020 19:15:18: 5000000 INFO @ Sun, 21 Jun 2020 19:15:22: 10000000 INFO @ Sun, 21 Jun 2020 19:15:23: 15000000 INFO @ Sun, 21 Jun 2020 19:15:25: 6000000 INFO @ Sun, 21 Jun 2020 19:15:30: 11000000 INFO @ Sun, 21 Jun 2020 19:15:30: 16000000 INFO @ Sun, 21 Jun 2020 19:15:33: 7000000 INFO @ Sun, 21 Jun 2020 19:15:34: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:15:34: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:15:34: #1 total tags in treatment: 16501822 INFO @ Sun, 21 Jun 2020 19:15:34: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:15:34: #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 19:15:34: #1 tags after filtering in treatment: 16501822 INFO @ Sun, 21 Jun 2020 19:15:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:15:34: #1 finished! INFO @ Sun, 21 Jun 2020 19:15:34: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:15:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:15:36: #2 number of paired peaks: 453 WARNING @ Sun, 21 Jun 2020 19:15:36: Fewer paired peaks (453) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 453 pairs to build model! INFO @ Sun, 21 Jun 2020 19:15:36: start model_add_line... INFO @ Sun, 21 Jun 2020 19:15:36: start X-correlation... INFO @ Sun, 21 Jun 2020 19:15:36: end of X-cor INFO @ Sun, 21 Jun 2020 19:15:36: #2 finished! INFO @ Sun, 21 Jun 2020 19:15:36: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 19:15:36: #2 alternative fragment length(s) may be 2,40,577 bps INFO @ Sun, 21 Jun 2020 19:15:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287778/SRX287778.05_model.r WARNING @ Sun, 21 Jun 2020 19:15:36: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:15:36: #2 You may need to consider one of the other alternative d(s): 2,40,577 WARNING @ Sun, 21 Jun 2020 19:15:36: #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 19:15:36: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:15:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:15:37: 12000000 INFO @ Sun, 21 Jun 2020 19:15:40: 8000000 INFO @ Sun, 21 Jun 2020 19:15:44: 13000000 INFO @ Sun, 21 Jun 2020 19:15:47: 9000000 INFO @ Sun, 21 Jun 2020 19:15:52: 14000000 INFO @ Sun, 21 Jun 2020 19:15:54: 10000000 INFO @ Sun, 21 Jun 2020 19:15:59: 15000000 INFO @ Sun, 21 Jun 2020 19:16:01: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:16:06: 16000000 INFO @ Sun, 21 Jun 2020 19:16:08: 12000000 INFO @ Sun, 21 Jun 2020 19:16:09: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:16:10: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:16:10: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:16:10: #1 total tags in treatment: 16501822 INFO @ Sun, 21 Jun 2020 19:16:10: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:16:10: #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 19:16:11: #1 tags after filtering in treatment: 16501822 INFO @ Sun, 21 Jun 2020 19:16:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:16:11: #1 finished! INFO @ Sun, 21 Jun 2020 19:16:11: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:16:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:16:12: #2 number of paired peaks: 453 WARNING @ Sun, 21 Jun 2020 19:16:12: Fewer paired peaks (453) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 453 pairs to build model! INFO @ Sun, 21 Jun 2020 19:16:12: start model_add_line... INFO @ Sun, 21 Jun 2020 19:16:12: start X-correlation... INFO @ Sun, 21 Jun 2020 19:16:12: end of X-cor INFO @ Sun, 21 Jun 2020 19:16:12: #2 finished! INFO @ Sun, 21 Jun 2020 19:16:12: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 19:16:12: #2 alternative fragment length(s) may be 2,40,577 bps INFO @ Sun, 21 Jun 2020 19:16:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287778/SRX287778.10_model.r WARNING @ Sun, 21 Jun 2020 19:16:12: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:16:12: #2 You may need to consider one of the other alternative d(s): 2,40,577 WARNING @ Sun, 21 Jun 2020 19:16:12: #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 19:16:12: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:16:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:16:15: 13000000 INFO @ Sun, 21 Jun 2020 19:16:22: 14000000 INFO @ Sun, 21 Jun 2020 19:16:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287778/SRX287778.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:16:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287778/SRX287778.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:16:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287778/SRX287778.05_summits.bed INFO @ Sun, 21 Jun 2020 19:16:25: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:16:29: 15000000 INFO @ Sun, 21 Jun 2020 19:16:35: 16000000 INFO @ Sun, 21 Jun 2020 19:16:39: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:16:39: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:16:39: #1 total tags in treatment: 16501822 INFO @ Sun, 21 Jun 2020 19:16:39: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:16:39: #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 19:16:39: #1 tags after filtering in treatment: 16501822 INFO @ Sun, 21 Jun 2020 19:16:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:16:39: #1 finished! INFO @ Sun, 21 Jun 2020 19:16:39: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:16:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:16:40: #2 number of paired peaks: 453 WARNING @ Sun, 21 Jun 2020 19:16:40: Fewer paired peaks (453) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 453 pairs to build model! INFO @ Sun, 21 Jun 2020 19:16:40: start model_add_line... INFO @ Sun, 21 Jun 2020 19:16:40: start X-correlation... INFO @ Sun, 21 Jun 2020 19:16:40: end of X-cor INFO @ Sun, 21 Jun 2020 19:16:40: #2 finished! INFO @ Sun, 21 Jun 2020 19:16:40: #2 predicted fragment length is 2 bps INFO @ Sun, 21 Jun 2020 19:16:40: #2 alternative fragment length(s) may be 2,40,577 bps INFO @ Sun, 21 Jun 2020 19:16:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287778/SRX287778.20_model.r WARNING @ Sun, 21 Jun 2020 19:16:40: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:16:40: #2 You may need to consider one of the other alternative d(s): 2,40,577 WARNING @ Sun, 21 Jun 2020 19:16:40: #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 19:16:40: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:16:40: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:16:44: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:17:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287778/SRX287778.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:17:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287778/SRX287778.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:17:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287778/SRX287778.10_summits.bed INFO @ Sun, 21 Jun 2020 19:17:01: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:17:15: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:17:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287778/SRX287778.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:17:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287778/SRX287778.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:17:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287778/SRX287778.20_summits.bed INFO @ Sun, 21 Jun 2020 19:17:30: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling