Job ID = 6453023 SRX = SRX099862 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:54:15 prefetch.2.10.7: 1) Downloading 'SRR350872'... 2020-06-21T07:54:15 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:56:03 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:56:03 prefetch.2.10.7: 1) 'SRR350872' was downloaded successfully Read 21433507 spots for SRR350872/SRR350872.sra Written 21433507 spots for SRR350872/SRR350872.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: 00:00:01 Multiseed full-index search: 00:05:19 21433507 reads; of these: 21433507 (100.00%) were unpaired; of these: 616630 (2.88%) aligned 0 times 16492023 (76.95%) aligned exactly 1 time 4324854 (20.18%) aligned >1 times 97.12% overall alignment rate Time searching: 00:05:20 Overall time: 00:05:20 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] 4412799 / 20816877 = 0.2120 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 17:07:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX099862/SRX099862.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX099862/SRX099862.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX099862/SRX099862.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX099862/SRX099862.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 17:07:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:07:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:07:52: 1000000 INFO @ Sun, 21 Jun 2020 17:07:57: 2000000 INFO @ Sun, 21 Jun 2020 17:08:02: 3000000 INFO @ Sun, 21 Jun 2020 17:08:07: 4000000 INFO @ Sun, 21 Jun 2020 17:08:12: 5000000 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 17:08:17: 6000000 INFO @ Sun, 21 Jun 2020 17:08:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX099862/SRX099862.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX099862/SRX099862.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX099862/SRX099862.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX099862/SRX099862.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 17:08:17: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:08:17: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:08:22: 7000000 INFO @ Sun, 21 Jun 2020 17:08:22: 1000000 INFO @ Sun, 21 Jun 2020 17:08:27: 8000000 INFO @ Sun, 21 Jun 2020 17:08:27: 2000000 INFO @ Sun, 21 Jun 2020 17:08:32: 9000000 INFO @ Sun, 21 Jun 2020 17:08:32: 3000000 INFO @ Sun, 21 Jun 2020 17:08:37: 10000000 INFO @ Sun, 21 Jun 2020 17:08:38: 4000000 INFO @ Sun, 21 Jun 2020 17:08:42: 11000000 INFO @ Sun, 21 Jun 2020 17:08:43: 5000000 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 17:08:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX099862/SRX099862.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX099862/SRX099862.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX099862/SRX099862.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX099862/SRX099862.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 17:08:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:08:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:08:47: 12000000 INFO @ Sun, 21 Jun 2020 17:08:48: 6000000 INFO @ Sun, 21 Jun 2020 17:08:52: 1000000 INFO @ Sun, 21 Jun 2020 17:08:52: 13000000 INFO @ Sun, 21 Jun 2020 17:08:53: 7000000 INFO @ Sun, 21 Jun 2020 17:08:58: 8000000 INFO @ Sun, 21 Jun 2020 17:08:58: 2000000 INFO @ Sun, 21 Jun 2020 17:08:58: 14000000 INFO @ Sun, 21 Jun 2020 17:09:03: 9000000 INFO @ Sun, 21 Jun 2020 17:09:03: 15000000 INFO @ Sun, 21 Jun 2020 17:09:03: 3000000 INFO @ Sun, 21 Jun 2020 17:09:08: 10000000 INFO @ Sun, 21 Jun 2020 17:09:08: 16000000 INFO @ Sun, 21 Jun 2020 17:09:08: 4000000 INFO @ Sun, 21 Jun 2020 17:09:11: #1 tag size is determined as 44 bps INFO @ Sun, 21 Jun 2020 17:09:11: #1 tag size = 44 INFO @ Sun, 21 Jun 2020 17:09:11: #1 total tags in treatment: 16404078 INFO @ Sun, 21 Jun 2020 17:09:11: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:09:11: #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 17:09:11: #1 tags after filtering in treatment: 16404076 INFO @ Sun, 21 Jun 2020 17:09:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:09:11: #1 finished! INFO @ Sun, 21 Jun 2020 17:09:11: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:09:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:09:12: #2 number of paired peaks: 126 WARNING @ Sun, 21 Jun 2020 17:09:12: Fewer paired peaks (126) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 126 pairs to build model! INFO @ Sun, 21 Jun 2020 17:09:12: start model_add_line... INFO @ Sun, 21 Jun 2020 17:09:12: start X-correlation... INFO @ Sun, 21 Jun 2020 17:09:12: end of X-cor INFO @ Sun, 21 Jun 2020 17:09:12: #2 finished! INFO @ Sun, 21 Jun 2020 17:09:12: #2 predicted fragment length is 3 bps INFO @ Sun, 21 Jun 2020 17:09:12: #2 alternative fragment length(s) may be 3,10,27,44,558,586 bps INFO @ Sun, 21 Jun 2020 17:09:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX099862/SRX099862.05_model.r WARNING @ Sun, 21 Jun 2020 17:09:12: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:09:12: #2 You may need to consider one of the other alternative d(s): 3,10,27,44,558,586 WARNING @ Sun, 21 Jun 2020 17:09:12: #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 17:09:12: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:09:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:09:13: 11000000 INFO @ Sun, 21 Jun 2020 17:09:13: 5000000 INFO @ Sun, 21 Jun 2020 17:09:18: 12000000 INFO @ Sun, 21 Jun 2020 17:09:19: 6000000 INFO @ Sun, 21 Jun 2020 17:09:23: 13000000 INFO @ Sun, 21 Jun 2020 17:09:24: 7000000 INFO @ Sun, 21 Jun 2020 17:09:28: 14000000 INFO @ Sun, 21 Jun 2020 17:09:29: 8000000 INFO @ Sun, 21 Jun 2020 17:09:33: 15000000 INFO @ Sun, 21 Jun 2020 17:09:34: 9000000 INFO @ Sun, 21 Jun 2020 17:09:38: 16000000 INFO @ Sun, 21 Jun 2020 17:09:39: 10000000 INFO @ Sun, 21 Jun 2020 17:09:40: #1 tag size is determined as 44 bps INFO @ Sun, 21 Jun 2020 17:09:40: #1 tag size = 44 INFO @ Sun, 21 Jun 2020 17:09:40: #1 total tags in treatment: 16404078 INFO @ Sun, 21 Jun 2020 17:09:40: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:09:40: #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 17:09:41: #1 tags after filtering in treatment: 16404076 INFO @ Sun, 21 Jun 2020 17:09:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:09:41: #1 finished! INFO @ Sun, 21 Jun 2020 17:09:41: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:09:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:09:42: #2 number of paired peaks: 126 WARNING @ Sun, 21 Jun 2020 17:09:42: Fewer paired peaks (126) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 126 pairs to build model! INFO @ Sun, 21 Jun 2020 17:09:42: start model_add_line... INFO @ Sun, 21 Jun 2020 17:09:42: start X-correlation... INFO @ Sun, 21 Jun 2020 17:09:42: end of X-cor INFO @ Sun, 21 Jun 2020 17:09:42: #2 finished! INFO @ Sun, 21 Jun 2020 17:09:42: #2 predicted fragment length is 3 bps INFO @ Sun, 21 Jun 2020 17:09:42: #2 alternative fragment length(s) may be 3,10,27,44,558,586 bps INFO @ Sun, 21 Jun 2020 17:09:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX099862/SRX099862.10_model.r WARNING @ Sun, 21 Jun 2020 17:09:42: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:09:42: #2 You may need to consider one of the other alternative d(s): 3,10,27,44,558,586 WARNING @ Sun, 21 Jun 2020 17:09:42: #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 17:09:42: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:09:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:09:44: 11000000 INFO @ Sun, 21 Jun 2020 17:09:46: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:09:50: 12000000 INFO @ Sun, 21 Jun 2020 17:09:55: 13000000 INFO @ Sun, 21 Jun 2020 17:10:01: 14000000 INFO @ Sun, 21 Jun 2020 17:10:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX099862/SRX099862.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:10:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX099862/SRX099862.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:10:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX099862/SRX099862.05_summits.bed INFO @ Sun, 21 Jun 2020 17:10:02: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:10:06: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:10:11: 16000000 INFO @ Sun, 21 Jun 2020 17:10:13: #1 tag size is determined as 44 bps INFO @ Sun, 21 Jun 2020 17:10:13: #1 tag size = 44 INFO @ Sun, 21 Jun 2020 17:10:13: #1 total tags in treatment: 16404078 INFO @ Sun, 21 Jun 2020 17:10:13: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:10:13: #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 17:10:14: #1 tags after filtering in treatment: 16404076 INFO @ Sun, 21 Jun 2020 17:10:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:10:14: #1 finished! INFO @ Sun, 21 Jun 2020 17:10:14: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:10:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:10:15: #2 number of paired peaks: 126 WARNING @ Sun, 21 Jun 2020 17:10:15: Fewer paired peaks (126) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 126 pairs to build model! INFO @ Sun, 21 Jun 2020 17:10:15: start model_add_line... INFO @ Sun, 21 Jun 2020 17:10:15: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:10:15: start X-correlation... INFO @ Sun, 21 Jun 2020 17:10:15: end of X-cor INFO @ Sun, 21 Jun 2020 17:10:15: #2 finished! INFO @ Sun, 21 Jun 2020 17:10:15: #2 predicted fragment length is 3 bps INFO @ Sun, 21 Jun 2020 17:10:15: #2 alternative fragment length(s) may be 3,10,27,44,558,586 bps INFO @ Sun, 21 Jun 2020 17:10:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX099862/SRX099862.20_model.r WARNING @ Sun, 21 Jun 2020 17:10:15: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:10:15: #2 You may need to consider one of the other alternative d(s): 3,10,27,44,558,586 WARNING @ Sun, 21 Jun 2020 17:10:15: #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 17:10:15: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:10:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:10:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX099862/SRX099862.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:10:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX099862/SRX099862.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:10:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX099862/SRX099862.10_summits.bed INFO @ Sun, 21 Jun 2020 17:10:31: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:10:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:11:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX099862/SRX099862.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:11:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX099862/SRX099862.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:11:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX099862/SRX099862.20_summits.bed INFO @ Sun, 21 Jun 2020 17:11:03: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling