Job ID = 6529452 SRX = SRX287583 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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: 00:06:52 22109731 reads; of these: 22109731 (100.00%) were unpaired; of these: 1594108 (7.21%) aligned 0 times 13930059 (63.00%) aligned exactly 1 time 6585564 (29.79%) aligned >1 times 92.79% overall alignment rate Time searching: 00:06:52 Overall time: 00:06:52 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] 4221342 / 20515623 = 0.2058 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 @ Tue, 30 Jun 2020 02:13:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287583/SRX287583.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287583/SRX287583.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287583/SRX287583.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287583/SRX287583.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 @ Tue, 30 Jun 2020 02:13:51: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:13:51: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:13:57: 1000000 INFO @ Tue, 30 Jun 2020 02:14:03: 2000000 INFO @ Tue, 30 Jun 2020 02:14:08: 3000000 INFO @ Tue, 30 Jun 2020 02:14:14: 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 @ Tue, 30 Jun 2020 02:14:20: 5000000 INFO @ Tue, 30 Jun 2020 02:14:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287583/SRX287583.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287583/SRX287583.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287583/SRX287583.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287583/SRX287583.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 @ Tue, 30 Jun 2020 02:14:21: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:14:21: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:14:26: 6000000 INFO @ Tue, 30 Jun 2020 02:14:27: 1000000 INFO @ Tue, 30 Jun 2020 02:14:32: 7000000 INFO @ Tue, 30 Jun 2020 02:14:34: 2000000 INFO @ Tue, 30 Jun 2020 02:14:38: 8000000 INFO @ Tue, 30 Jun 2020 02:14:40: 3000000 INFO @ Tue, 30 Jun 2020 02:14:44: 9000000 INFO @ Tue, 30 Jun 2020 02:14:46: 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 @ Tue, 30 Jun 2020 02:14:50: 10000000 INFO @ Tue, 30 Jun 2020 02:14:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287583/SRX287583.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287583/SRX287583.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287583/SRX287583.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287583/SRX287583.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 @ Tue, 30 Jun 2020 02:14:51: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:14:51: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:14:52: 5000000 INFO @ Tue, 30 Jun 2020 02:14:57: 11000000 INFO @ Tue, 30 Jun 2020 02:14:58: 1000000 INFO @ Tue, 30 Jun 2020 02:14:59: 6000000 INFO @ Tue, 30 Jun 2020 02:15:03: 12000000 INFO @ Tue, 30 Jun 2020 02:15:04: 2000000 INFO @ Tue, 30 Jun 2020 02:15:05: 7000000 INFO @ Tue, 30 Jun 2020 02:15:10: 13000000 INFO @ Tue, 30 Jun 2020 02:15:11: 3000000 INFO @ Tue, 30 Jun 2020 02:15:12: 8000000 INFO @ Tue, 30 Jun 2020 02:15:17: 14000000 INFO @ Tue, 30 Jun 2020 02:15:18: 4000000 INFO @ Tue, 30 Jun 2020 02:15:19: 9000000 INFO @ Tue, 30 Jun 2020 02:15:24: 15000000 INFO @ Tue, 30 Jun 2020 02:15:24: 5000000 INFO @ Tue, 30 Jun 2020 02:15:25: 10000000 INFO @ Tue, 30 Jun 2020 02:15:30: 16000000 INFO @ Tue, 30 Jun 2020 02:15:31: 6000000 INFO @ Tue, 30 Jun 2020 02:15:32: 11000000 INFO @ Tue, 30 Jun 2020 02:15:33: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:15:33: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:15:33: #1 total tags in treatment: 16294281 INFO @ Tue, 30 Jun 2020 02:15:33: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:15:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:15:33: #1 tags after filtering in treatment: 16294281 INFO @ Tue, 30 Jun 2020 02:15:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:15:33: #1 finished! INFO @ Tue, 30 Jun 2020 02:15:33: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:15:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:15:34: #2 number of paired peaks: 712 WARNING @ Tue, 30 Jun 2020 02:15:34: Fewer paired peaks (712) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 712 pairs to build model! INFO @ Tue, 30 Jun 2020 02:15:34: start model_add_line... INFO @ Tue, 30 Jun 2020 02:15:35: start X-correlation... INFO @ Tue, 30 Jun 2020 02:15:35: end of X-cor INFO @ Tue, 30 Jun 2020 02:15:35: #2 finished! INFO @ Tue, 30 Jun 2020 02:15:35: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 02:15:35: #2 alternative fragment length(s) may be 2,34 bps INFO @ Tue, 30 Jun 2020 02:15:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287583/SRX287583.05_model.r WARNING @ Tue, 30 Jun 2020 02:15:35: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:15:35: #2 You may need to consider one of the other alternative d(s): 2,34 WARNING @ Tue, 30 Jun 2020 02:15:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:15:35: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:15:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:15:37: 7000000 INFO @ Tue, 30 Jun 2020 02:15:38: 12000000 INFO @ Tue, 30 Jun 2020 02:15:43: 8000000 INFO @ Tue, 30 Jun 2020 02:15:45: 13000000 INFO @ Tue, 30 Jun 2020 02:15:49: 9000000 INFO @ Tue, 30 Jun 2020 02:15:51: 14000000 INFO @ Tue, 30 Jun 2020 02:15:55: 10000000 INFO @ Tue, 30 Jun 2020 02:15:57: 15000000 INFO @ Tue, 30 Jun 2020 02:16:01: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:16:02: 11000000 INFO @ Tue, 30 Jun 2020 02:16:04: 16000000 INFO @ Tue, 30 Jun 2020 02:16:06: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:16:06: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:16:06: #1 total tags in treatment: 16294281 INFO @ Tue, 30 Jun 2020 02:16:06: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:16:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:16:06: #1 tags after filtering in treatment: 16294281 INFO @ Tue, 30 Jun 2020 02:16:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:16:06: #1 finished! INFO @ Tue, 30 Jun 2020 02:16:06: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:16:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:16:07: 12000000 INFO @ Tue, 30 Jun 2020 02:16:08: #2 number of paired peaks: 712 WARNING @ Tue, 30 Jun 2020 02:16:08: Fewer paired peaks (712) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 712 pairs to build model! INFO @ Tue, 30 Jun 2020 02:16:08: start model_add_line... INFO @ Tue, 30 Jun 2020 02:16:08: start X-correlation... INFO @ Tue, 30 Jun 2020 02:16:08: end of X-cor INFO @ Tue, 30 Jun 2020 02:16:08: #2 finished! INFO @ Tue, 30 Jun 2020 02:16:08: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 02:16:08: #2 alternative fragment length(s) may be 2,34 bps INFO @ Tue, 30 Jun 2020 02:16:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287583/SRX287583.10_model.r WARNING @ Tue, 30 Jun 2020 02:16:08: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:16:08: #2 You may need to consider one of the other alternative d(s): 2,34 WARNING @ Tue, 30 Jun 2020 02:16:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:16:08: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:16:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:16:14: 13000000 INFO @ Tue, 30 Jun 2020 02:16:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287583/SRX287583.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:16:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287583/SRX287583.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:16:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287583/SRX287583.05_summits.bed INFO @ Tue, 30 Jun 2020 02:16:15: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:16:19: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:16:25: 15000000 INFO @ Tue, 30 Jun 2020 02:16:31: 16000000 INFO @ Tue, 30 Jun 2020 02:16:33: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:16:33: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:16:33: #1 total tags in treatment: 16294281 INFO @ Tue, 30 Jun 2020 02:16:33: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:16:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:16:34: #1 tags after filtering in treatment: 16294281 INFO @ Tue, 30 Jun 2020 02:16:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:16:34: #1 finished! INFO @ Tue, 30 Jun 2020 02:16:34: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:16:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:16:34: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:16:35: #2 number of paired peaks: 712 WARNING @ Tue, 30 Jun 2020 02:16:35: Fewer paired peaks (712) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 712 pairs to build model! INFO @ Tue, 30 Jun 2020 02:16:35: start model_add_line... INFO @ Tue, 30 Jun 2020 02:16:35: start X-correlation... INFO @ Tue, 30 Jun 2020 02:16:35: end of X-cor INFO @ Tue, 30 Jun 2020 02:16:35: #2 finished! INFO @ Tue, 30 Jun 2020 02:16:35: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 02:16:35: #2 alternative fragment length(s) may be 2,34 bps INFO @ Tue, 30 Jun 2020 02:16:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287583/SRX287583.20_model.r WARNING @ Tue, 30 Jun 2020 02:16:35: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:16:35: #2 You may need to consider one of the other alternative d(s): 2,34 WARNING @ Tue, 30 Jun 2020 02:16:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:16:35: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:16:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:16:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287583/SRX287583.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:16:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287583/SRX287583.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:16:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287583/SRX287583.10_summits.bed INFO @ Tue, 30 Jun 2020 02:16:48: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:17:02: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:17:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287583/SRX287583.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:17:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287583/SRX287583.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:17:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287583/SRX287583.20_summits.bed INFO @ Tue, 30 Jun 2020 02:17:15: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling