Job ID = 6456337 SRX = SRX336286 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:43:23 prefetch.2.10.7: 1) Downloading 'SRR953626'... 2020-06-21T10:43:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:46:38 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:46:39 prefetch.2.10.7: 'SRR953626' is valid 2020-06-21T10:46:39 prefetch.2.10.7: 1) 'SRR953626' was downloaded successfully Read 17232507 spots for SRR953626/SRR953626.sra Written 17232507 spots for SRR953626/SRR953626.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: 00:04:21 17232507 reads; of these: 17232507 (100.00%) were unpaired; of these: 337997 (1.96%) aligned 0 times 12617092 (73.22%) aligned exactly 1 time 4277418 (24.82%) aligned >1 times 98.04% overall alignment rate Time searching: 00:04:21 Overall time: 00:04:21 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] 3804864 / 16894510 = 0.2252 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 19:56:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX336286/SRX336286.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX336286/SRX336286.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX336286/SRX336286.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX336286/SRX336286.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 19:56:15: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:56:15: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:56:20: 1000000 INFO @ Sun, 21 Jun 2020 19:56:26: 2000000 INFO @ Sun, 21 Jun 2020 19:56:32: 3000000 INFO @ Sun, 21 Jun 2020 19:56:37: 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 19:56:43: 5000000 INFO @ Sun, 21 Jun 2020 19:56:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX336286/SRX336286.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX336286/SRX336286.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX336286/SRX336286.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX336286/SRX336286.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 19:56:45: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:56:45: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:56:49: 6000000 INFO @ Sun, 21 Jun 2020 19:56:51: 1000000 INFO @ Sun, 21 Jun 2020 19:56:55: 7000000 INFO @ Sun, 21 Jun 2020 19:56:57: 2000000 INFO @ Sun, 21 Jun 2020 19:57:02: 8000000 INFO @ Sun, 21 Jun 2020 19:57:04: 3000000 INFO @ Sun, 21 Jun 2020 19:57:08: 9000000 INFO @ Sun, 21 Jun 2020 19:57:10: 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 19:57:15: 10000000 INFO @ Sun, 21 Jun 2020 19:57:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX336286/SRX336286.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX336286/SRX336286.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX336286/SRX336286.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX336286/SRX336286.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 19:57:15: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:57:15: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:57:16: 5000000 INFO @ Sun, 21 Jun 2020 19:57:22: 11000000 INFO @ Sun, 21 Jun 2020 19:57:23: 6000000 INFO @ Sun, 21 Jun 2020 19:57:24: 1000000 INFO @ Sun, 21 Jun 2020 19:57:29: 12000000 INFO @ Sun, 21 Jun 2020 19:57:30: 7000000 INFO @ Sun, 21 Jun 2020 19:57:32: 2000000 INFO @ Sun, 21 Jun 2020 19:57:37: 13000000 INFO @ Sun, 21 Jun 2020 19:57:37: 8000000 INFO @ Sun, 21 Jun 2020 19:57:37: #1 tag size is determined as 44 bps INFO @ Sun, 21 Jun 2020 19:57:37: #1 tag size = 44 INFO @ Sun, 21 Jun 2020 19:57:37: #1 total tags in treatment: 13089646 INFO @ Sun, 21 Jun 2020 19:57:37: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:57:37: #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 19:57:38: #1 tags after filtering in treatment: 13089645 INFO @ Sun, 21 Jun 2020 19:57:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:57:38: #1 finished! INFO @ Sun, 21 Jun 2020 19:57:38: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:57:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:57:39: #2 number of paired peaks: 116 WARNING @ Sun, 21 Jun 2020 19:57:39: Fewer paired peaks (116) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 116 pairs to build model! INFO @ Sun, 21 Jun 2020 19:57:39: start model_add_line... INFO @ Sun, 21 Jun 2020 19:57:39: start X-correlation... INFO @ Sun, 21 Jun 2020 19:57:39: end of X-cor INFO @ Sun, 21 Jun 2020 19:57:39: #2 finished! INFO @ Sun, 21 Jun 2020 19:57:39: #2 predicted fragment length is 4 bps INFO @ Sun, 21 Jun 2020 19:57:39: #2 alternative fragment length(s) may be 4,44,64,114,284,323,547,572,593 bps INFO @ Sun, 21 Jun 2020 19:57:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX336286/SRX336286.05_model.r WARNING @ Sun, 21 Jun 2020 19:57:39: #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 19:57:39: #2 You may need to consider one of the other alternative d(s): 4,44,64,114,284,323,547,572,593 WARNING @ Sun, 21 Jun 2020 19:57:39: #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 19:57:39: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:57:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:57:41: 3000000 INFO @ Sun, 21 Jun 2020 19:57:44: 9000000 INFO @ Sun, 21 Jun 2020 19:57:49: 4000000 INFO @ Sun, 21 Jun 2020 19:57:51: 10000000 INFO @ Sun, 21 Jun 2020 19:57:57: 5000000 INFO @ Sun, 21 Jun 2020 19:57:58: 11000000 INFO @ Sun, 21 Jun 2020 19:58:05: 6000000 INFO @ Sun, 21 Jun 2020 19:58:05: 12000000 INFO @ Sun, 21 Jun 2020 19:58:07: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:58:12: 7000000 INFO @ Sun, 21 Jun 2020 19:58:13: 13000000 INFO @ Sun, 21 Jun 2020 19:58:13: #1 tag size is determined as 44 bps INFO @ Sun, 21 Jun 2020 19:58:13: #1 tag size = 44 INFO @ Sun, 21 Jun 2020 19:58:13: #1 total tags in treatment: 13089646 INFO @ Sun, 21 Jun 2020 19:58:13: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:58:13: #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 19:58:14: #1 tags after filtering in treatment: 13089645 INFO @ Sun, 21 Jun 2020 19:58:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:58:14: #1 finished! INFO @ Sun, 21 Jun 2020 19:58:14: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:58:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:58:15: #2 number of paired peaks: 116 WARNING @ Sun, 21 Jun 2020 19:58:15: Fewer paired peaks (116) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 116 pairs to build model! INFO @ Sun, 21 Jun 2020 19:58:15: start model_add_line... INFO @ Sun, 21 Jun 2020 19:58:15: start X-correlation... INFO @ Sun, 21 Jun 2020 19:58:15: end of X-cor INFO @ Sun, 21 Jun 2020 19:58:15: #2 finished! INFO @ Sun, 21 Jun 2020 19:58:15: #2 predicted fragment length is 4 bps INFO @ Sun, 21 Jun 2020 19:58:15: #2 alternative fragment length(s) may be 4,44,64,114,284,323,547,572,593 bps INFO @ Sun, 21 Jun 2020 19:58:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX336286/SRX336286.10_model.r WARNING @ Sun, 21 Jun 2020 19:58:15: #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 19:58:15: #2 You may need to consider one of the other alternative d(s): 4,44,64,114,284,323,547,572,593 WARNING @ Sun, 21 Jun 2020 19:58:15: #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 19:58:15: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:58:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:58:20: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:58:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX336286/SRX336286.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:58:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX336286/SRX336286.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:58:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX336286/SRX336286.05_summits.bed INFO @ Sun, 21 Jun 2020 19:58:21: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:58:27: 9000000 INFO @ Sun, 21 Jun 2020 19:58:33: 10000000 INFO @ Sun, 21 Jun 2020 19:58:41: 11000000 INFO @ Sun, 21 Jun 2020 19:58:43: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:58:47: 12000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:58:54: 13000000 INFO @ Sun, 21 Jun 2020 19:58:55: #1 tag size is determined as 44 bps INFO @ Sun, 21 Jun 2020 19:58:55: #1 tag size = 44 INFO @ Sun, 21 Jun 2020 19:58:55: #1 total tags in treatment: 13089646 INFO @ Sun, 21 Jun 2020 19:58:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:58:55: #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 19:58:55: #1 tags after filtering in treatment: 13089645 INFO @ Sun, 21 Jun 2020 19:58:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:58:55: #1 finished! INFO @ Sun, 21 Jun 2020 19:58:55: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:58:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:58:56: #2 number of paired peaks: 116 WARNING @ Sun, 21 Jun 2020 19:58:56: Fewer paired peaks (116) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 116 pairs to build model! INFO @ Sun, 21 Jun 2020 19:58:56: start model_add_line... INFO @ Sun, 21 Jun 2020 19:58:56: start X-correlation... INFO @ Sun, 21 Jun 2020 19:58:56: end of X-cor INFO @ Sun, 21 Jun 2020 19:58:56: #2 finished! INFO @ Sun, 21 Jun 2020 19:58:56: #2 predicted fragment length is 4 bps INFO @ Sun, 21 Jun 2020 19:58:56: #2 alternative fragment length(s) may be 4,44,64,114,284,323,547,572,593 bps INFO @ Sun, 21 Jun 2020 19:58:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX336286/SRX336286.20_model.r WARNING @ Sun, 21 Jun 2020 19:58:56: #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 19:58:56: #2 You may need to consider one of the other alternative d(s): 4,44,64,114,284,323,547,572,593 WARNING @ Sun, 21 Jun 2020 19:58:56: #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 19:58:56: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:58:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:58:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX336286/SRX336286.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:58:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX336286/SRX336286.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:58:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX336286/SRX336286.10_summits.bed INFO @ Sun, 21 Jun 2020 19:58:57: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:59:23: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:59:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX336286/SRX336286.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:59:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX336286/SRX336286.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:59:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX336286/SRX336286.20_summits.bed INFO @ Sun, 21 Jun 2020 19:59:36: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling