Job ID = 6456327 SRX = SRX336279 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:38:44 prefetch.2.10.7: 1) Downloading 'SRR953619'... 2020-06-21T10:38:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:42:19 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:42:19 prefetch.2.10.7: 1) 'SRR953619' was downloaded successfully Read 19141145 spots for SRR953619/SRR953619.sra Written 19141145 spots for SRR953619/SRR953619.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: 00:03:31 19141145 reads; of these: 19141145 (100.00%) were unpaired; of these: 2487311 (12.99%) aligned 0 times 14907565 (77.88%) aligned exactly 1 time 1746269 (9.12%) aligned >1 times 87.01% overall alignment rate Time searching: 00:03:31 Overall time: 00:03:31 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] 3109868 / 16653834 = 0.1867 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 19:50:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX336279/SRX336279.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX336279/SRX336279.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX336279/SRX336279.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX336279/SRX336279.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 19:50:42: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:50:42: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:50:48: 1000000 INFO @ Sun, 21 Jun 2020 19:50:53: 2000000 INFO @ Sun, 21 Jun 2020 19:50:59: 3000000 INFO @ Sun, 21 Jun 2020 19:51:04: 4000000 INFO @ Sun, 21 Jun 2020 19:51:09: 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 19:51:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX336279/SRX336279.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX336279/SRX336279.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX336279/SRX336279.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX336279/SRX336279.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 19:51:12: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:51:12: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:51:15: 6000000 INFO @ Sun, 21 Jun 2020 19:51:19: 1000000 INFO @ Sun, 21 Jun 2020 19:51:21: 7000000 INFO @ Sun, 21 Jun 2020 19:51:25: 2000000 INFO @ Sun, 21 Jun 2020 19:51:27: 8000000 INFO @ Sun, 21 Jun 2020 19:51:31: 3000000 INFO @ Sun, 21 Jun 2020 19:51:33: 9000000 INFO @ Sun, 21 Jun 2020 19:51:37: 4000000 INFO @ Sun, 21 Jun 2020 19:51:39: 10000000 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 19:51:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX336279/SRX336279.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX336279/SRX336279.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX336279/SRX336279.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX336279/SRX336279.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 19:51:42: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:51:42: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:51:43: 5000000 INFO @ Sun, 21 Jun 2020 19:51:46: 11000000 INFO @ Sun, 21 Jun 2020 19:51:49: 1000000 INFO @ Sun, 21 Jun 2020 19:51:49: 6000000 INFO @ Sun, 21 Jun 2020 19:51:52: 12000000 INFO @ Sun, 21 Jun 2020 19:51:55: 2000000 INFO @ Sun, 21 Jun 2020 19:51:55: 7000000 INFO @ Sun, 21 Jun 2020 19:51:58: 13000000 INFO @ Sun, 21 Jun 2020 19:52:01: 3000000 INFO @ Sun, 21 Jun 2020 19:52:02: 8000000 INFO @ Sun, 21 Jun 2020 19:52:02: #1 tag size is determined as 44 bps INFO @ Sun, 21 Jun 2020 19:52:02: #1 tag size = 44 INFO @ Sun, 21 Jun 2020 19:52:02: #1 total tags in treatment: 13543966 INFO @ Sun, 21 Jun 2020 19:52:02: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:52:02: #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 19:52:02: #1 tags after filtering in treatment: 13543900 INFO @ Sun, 21 Jun 2020 19:52:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:52:02: #1 finished! INFO @ Sun, 21 Jun 2020 19:52:02: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:52:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:52:03: #2 number of paired peaks: 124 WARNING @ Sun, 21 Jun 2020 19:52:03: Fewer paired peaks (124) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 124 pairs to build model! INFO @ Sun, 21 Jun 2020 19:52:03: start model_add_line... INFO @ Sun, 21 Jun 2020 19:52:03: start X-correlation... INFO @ Sun, 21 Jun 2020 19:52:03: end of X-cor INFO @ Sun, 21 Jun 2020 19:52:03: #2 finished! INFO @ Sun, 21 Jun 2020 19:52:03: #2 predicted fragment length is 4 bps INFO @ Sun, 21 Jun 2020 19:52:03: #2 alternative fragment length(s) may be 4,37,70 bps INFO @ Sun, 21 Jun 2020 19:52:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX336279/SRX336279.05_model.r WARNING @ Sun, 21 Jun 2020 19:52:03: #2 Since the d (4) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:52:03: #2 You may need to consider one of the other alternative d(s): 4,37,70 WARNING @ Sun, 21 Jun 2020 19:52:03: #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 19:52:03: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:52:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:52:07: 4000000 INFO @ Sun, 21 Jun 2020 19:52:08: 9000000 INFO @ Sun, 21 Jun 2020 19:52:14: 5000000 INFO @ Sun, 21 Jun 2020 19:52:14: 10000000 INFO @ Sun, 21 Jun 2020 19:52:20: 6000000 INFO @ Sun, 21 Jun 2020 19:52:20: 11000000 INFO @ Sun, 21 Jun 2020 19:52:26: 7000000 INFO @ Sun, 21 Jun 2020 19:52:27: 12000000 INFO @ Sun, 21 Jun 2020 19:52:29: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:52:32: 8000000 INFO @ Sun, 21 Jun 2020 19:52:33: 13000000 INFO @ Sun, 21 Jun 2020 19:52:36: #1 tag size is determined as 44 bps INFO @ Sun, 21 Jun 2020 19:52:36: #1 tag size = 44 INFO @ Sun, 21 Jun 2020 19:52:36: #1 total tags in treatment: 13543966 INFO @ Sun, 21 Jun 2020 19:52:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:52:36: #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 19:52:37: #1 tags after filtering in treatment: 13543900 INFO @ Sun, 21 Jun 2020 19:52:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:52:37: #1 finished! INFO @ Sun, 21 Jun 2020 19:52:37: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:52:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:52:38: #2 number of paired peaks: 124 WARNING @ Sun, 21 Jun 2020 19:52:38: Fewer paired peaks (124) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 124 pairs to build model! INFO @ Sun, 21 Jun 2020 19:52:38: start model_add_line... INFO @ Sun, 21 Jun 2020 19:52:38: start X-correlation... INFO @ Sun, 21 Jun 2020 19:52:38: end of X-cor INFO @ Sun, 21 Jun 2020 19:52:38: #2 finished! INFO @ Sun, 21 Jun 2020 19:52:38: #2 predicted fragment length is 4 bps INFO @ Sun, 21 Jun 2020 19:52:38: #2 alternative fragment length(s) may be 4,37,70 bps INFO @ Sun, 21 Jun 2020 19:52:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX336279/SRX336279.10_model.r WARNING @ Sun, 21 Jun 2020 19:52:38: #2 Since the d (4) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:52:38: #2 You may need to consider one of the other alternative d(s): 4,37,70 WARNING @ Sun, 21 Jun 2020 19:52:38: #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 19:52:38: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:52:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:52:38: 9000000 INFO @ Sun, 21 Jun 2020 19:52:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX336279/SRX336279.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:52:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX336279/SRX336279.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:52:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX336279/SRX336279.05_summits.bed INFO @ Sun, 21 Jun 2020 19:52:42: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:52:43: 10000000 INFO @ Sun, 21 Jun 2020 19:52:49: 11000000 INFO @ Sun, 21 Jun 2020 19:52:54: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:53:00: 13000000 INFO @ Sun, 21 Jun 2020 19:53:03: #1 tag size is determined as 44 bps INFO @ Sun, 21 Jun 2020 19:53:03: #1 tag size = 44 INFO @ Sun, 21 Jun 2020 19:53:03: #1 total tags in treatment: 13543966 INFO @ Sun, 21 Jun 2020 19:53:03: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:53:03: #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 19:53:04: #1 tags after filtering in treatment: 13543900 INFO @ Sun, 21 Jun 2020 19:53:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:53:04: #1 finished! INFO @ Sun, 21 Jun 2020 19:53:04: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:53:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:53:05: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:53:05: #2 number of paired peaks: 124 WARNING @ Sun, 21 Jun 2020 19:53:05: Fewer paired peaks (124) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 124 pairs to build model! INFO @ Sun, 21 Jun 2020 19:53:05: start model_add_line... INFO @ Sun, 21 Jun 2020 19:53:05: start X-correlation... INFO @ Sun, 21 Jun 2020 19:53:05: end of X-cor INFO @ Sun, 21 Jun 2020 19:53:05: #2 finished! INFO @ Sun, 21 Jun 2020 19:53:05: #2 predicted fragment length is 4 bps INFO @ Sun, 21 Jun 2020 19:53:05: #2 alternative fragment length(s) may be 4,37,70 bps INFO @ Sun, 21 Jun 2020 19:53:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX336279/SRX336279.20_model.r WARNING @ Sun, 21 Jun 2020 19:53:05: #2 Since the d (4) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:53:05: #2 You may need to consider one of the other alternative d(s): 4,37,70 WARNING @ Sun, 21 Jun 2020 19:53:05: #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 19:53:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:53:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:53:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX336279/SRX336279.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:53:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX336279/SRX336279.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:53:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX336279/SRX336279.10_summits.bed INFO @ Sun, 21 Jun 2020 19:53:18: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:53:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:53:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX336279/SRX336279.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:53:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX336279/SRX336279.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:53:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX336279/SRX336279.20_summits.bed INFO @ Sun, 21 Jun 2020 19:53:46: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling