Job ID = 6529247 SRX = SRX110792 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: 00:04:43 13987340 reads; of these: 13987340 (100.00%) were unpaired; of these: 285319 (2.04%) aligned 0 times 6690646 (47.83%) aligned exactly 1 time 7011375 (50.13%) aligned >1 times 97.96% overall alignment rate Time searching: 00:04:44 Overall time: 00:04:44 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_rmdupse_core] 1084559 / 13702021 = 0.0792 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 01:57:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX110792/SRX110792.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX110792/SRX110792.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX110792/SRX110792.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX110792/SRX110792.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 01:57:14: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:57:14: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:57:18: 1000000 INFO @ Tue, 30 Jun 2020 01:57:22: 2000000 INFO @ Tue, 30 Jun 2020 01:57:26: 3000000 INFO @ Tue, 30 Jun 2020 01:57:30: 4000000 INFO @ Tue, 30 Jun 2020 01:57:35: 5000000 INFO @ Tue, 30 Jun 2020 01:57:39: 6000000 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 01:57:43: 7000000 INFO @ Tue, 30 Jun 2020 01:57:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX110792/SRX110792.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX110792/SRX110792.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX110792/SRX110792.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX110792/SRX110792.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 01:57:44: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:57:44: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:57:47: 8000000 INFO @ Tue, 30 Jun 2020 01:57:48: 1000000 INFO @ Tue, 30 Jun 2020 01:57:51: 9000000 INFO @ Tue, 30 Jun 2020 01:57:53: 2000000 INFO @ Tue, 30 Jun 2020 01:57:55: 10000000 INFO @ Tue, 30 Jun 2020 01:57:57: 3000000 INFO @ Tue, 30 Jun 2020 01:58:00: 11000000 INFO @ Tue, 30 Jun 2020 01:58:01: 4000000 INFO @ Tue, 30 Jun 2020 01:58:04: 12000000 INFO @ Tue, 30 Jun 2020 01:58:05: 5000000 INFO @ Tue, 30 Jun 2020 01:58:07: #1 tag size is determined as 18 bps INFO @ Tue, 30 Jun 2020 01:58:07: #1 tag size = 18 INFO @ Tue, 30 Jun 2020 01:58:07: #1 total tags in treatment: 12617462 INFO @ Tue, 30 Jun 2020 01:58:07: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:58:07: #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 01:58:07: #1 tags after filtering in treatment: 12617461 INFO @ Tue, 30 Jun 2020 01:58:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:58:07: #1 finished! INFO @ Tue, 30 Jun 2020 01:58:07: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:58:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:58:08: #2 number of paired peaks: 248 WARNING @ Tue, 30 Jun 2020 01:58:08: Fewer paired peaks (248) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 248 pairs to build model! INFO @ Tue, 30 Jun 2020 01:58:08: start model_add_line... INFO @ Tue, 30 Jun 2020 01:58:08: start X-correlation... INFO @ Tue, 30 Jun 2020 01:58:08: end of X-cor INFO @ Tue, 30 Jun 2020 01:58:08: #2 finished! INFO @ Tue, 30 Jun 2020 01:58:08: #2 predicted fragment length is 23 bps INFO @ Tue, 30 Jun 2020 01:58:08: #2 alternative fragment length(s) may be 4,23,524 bps INFO @ Tue, 30 Jun 2020 01:58:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX110792/SRX110792.05_model.r WARNING @ Tue, 30 Jun 2020 01:58:08: #2 Since the d (23) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:58:08: #2 You may need to consider one of the other alternative d(s): 4,23,524 WARNING @ Tue, 30 Jun 2020 01:58:08: #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 01:58:08: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:58:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:58:10: 6000000 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 01:58:14: 7000000 INFO @ Tue, 30 Jun 2020 01:58:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX110792/SRX110792.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX110792/SRX110792.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX110792/SRX110792.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX110792/SRX110792.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 01:58:15: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:58:15: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:58:18: 8000000 INFO @ Tue, 30 Jun 2020 01:58:19: 1000000 INFO @ Tue, 30 Jun 2020 01:58:22: 9000000 INFO @ Tue, 30 Jun 2020 01:58:23: 2000000 INFO @ Tue, 30 Jun 2020 01:58:27: 10000000 INFO @ Tue, 30 Jun 2020 01:58:27: 3000000 INFO @ Tue, 30 Jun 2020 01:58:31: 11000000 INFO @ Tue, 30 Jun 2020 01:58:32: 4000000 INFO @ Tue, 30 Jun 2020 01:58:32: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:58:35: 12000000 INFO @ Tue, 30 Jun 2020 01:58:36: 5000000 INFO @ Tue, 30 Jun 2020 01:58:38: #1 tag size is determined as 18 bps INFO @ Tue, 30 Jun 2020 01:58:38: #1 tag size = 18 INFO @ Tue, 30 Jun 2020 01:58:38: #1 total tags in treatment: 12617462 INFO @ Tue, 30 Jun 2020 01:58:38: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:58:38: #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 01:58:39: #1 tags after filtering in treatment: 12617461 INFO @ Tue, 30 Jun 2020 01:58:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:58:39: #1 finished! INFO @ Tue, 30 Jun 2020 01:58:39: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:58:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:58:40: #2 number of paired peaks: 248 WARNING @ Tue, 30 Jun 2020 01:58:40: Fewer paired peaks (248) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 248 pairs to build model! INFO @ Tue, 30 Jun 2020 01:58:40: start model_add_line... INFO @ Tue, 30 Jun 2020 01:58:40: start X-correlation... INFO @ Tue, 30 Jun 2020 01:58:40: end of X-cor INFO @ Tue, 30 Jun 2020 01:58:40: #2 finished! INFO @ Tue, 30 Jun 2020 01:58:40: #2 predicted fragment length is 23 bps INFO @ Tue, 30 Jun 2020 01:58:40: #2 alternative fragment length(s) may be 4,23,524 bps INFO @ Tue, 30 Jun 2020 01:58:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX110792/SRX110792.10_model.r WARNING @ Tue, 30 Jun 2020 01:58:40: #2 Since the d (23) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:58:40: #2 You may need to consider one of the other alternative d(s): 4,23,524 WARNING @ Tue, 30 Jun 2020 01:58:40: #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 01:58:40: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:58:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:58:40: 6000000 INFO @ Tue, 30 Jun 2020 01:58:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX110792/SRX110792.05_peaks.xls INFO @ Tue, 30 Jun 2020 01:58:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX110792/SRX110792.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:58:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX110792/SRX110792.05_summits.bed INFO @ Tue, 30 Jun 2020 01:58:44: Done! INFO @ Tue, 30 Jun 2020 01:58:44: 7000000 pass1 - making usageList (446 chroms): 2 millis pass2 - checking and writing primary data (2416 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:58:49: 8000000 INFO @ Tue, 30 Jun 2020 01:58:53: 9000000 INFO @ Tue, 30 Jun 2020 01:58:57: 10000000 INFO @ Tue, 30 Jun 2020 01:59:02: 11000000 INFO @ Tue, 30 Jun 2020 01:59:04: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:59:06: 12000000 INFO @ Tue, 30 Jun 2020 01:59:08: #1 tag size is determined as 18 bps INFO @ Tue, 30 Jun 2020 01:59:08: #1 tag size = 18 INFO @ Tue, 30 Jun 2020 01:59:08: #1 total tags in treatment: 12617462 INFO @ Tue, 30 Jun 2020 01:59:08: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:59:08: #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 01:59:09: #1 tags after filtering in treatment: 12617461 INFO @ Tue, 30 Jun 2020 01:59:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:59:09: #1 finished! INFO @ Tue, 30 Jun 2020 01:59:09: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:59:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:59:10: #2 number of paired peaks: 248 WARNING @ Tue, 30 Jun 2020 01:59:10: Fewer paired peaks (248) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 248 pairs to build model! INFO @ Tue, 30 Jun 2020 01:59:10: start model_add_line... INFO @ Tue, 30 Jun 2020 01:59:10: start X-correlation... INFO @ Tue, 30 Jun 2020 01:59:10: end of X-cor INFO @ Tue, 30 Jun 2020 01:59:10: #2 finished! INFO @ Tue, 30 Jun 2020 01:59:10: #2 predicted fragment length is 23 bps INFO @ Tue, 30 Jun 2020 01:59:10: #2 alternative fragment length(s) may be 4,23,524 bps INFO @ Tue, 30 Jun 2020 01:59:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX110792/SRX110792.20_model.r WARNING @ Tue, 30 Jun 2020 01:59:10: #2 Since the d (23) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:59:10: #2 You may need to consider one of the other alternative d(s): 4,23,524 WARNING @ Tue, 30 Jun 2020 01:59:10: #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 01:59:10: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:59:10: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 01:59:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX110792/SRX110792.10_peaks.xls INFO @ Tue, 30 Jun 2020 01:59:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX110792/SRX110792.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:59:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX110792/SRX110792.10_summits.bed INFO @ Tue, 30 Jun 2020 01:59:16: Done! pass1 - making usageList (236 chroms): 1 millis pass2 - checking and writing primary data (537 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:59:34: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 01:59:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX110792/SRX110792.20_peaks.xls INFO @ Tue, 30 Jun 2020 01:59:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX110792/SRX110792.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:59:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX110792/SRX110792.20_summits.bed INFO @ Tue, 30 Jun 2020 01:59:46: Done! pass1 - making usageList (46 chroms): 1 millis pass2 - checking and writing primary data (98 records, 4 fields): 2 millis CompletedMACS2peakCalling