Job ID = 10166624 SRX = SRX9008801 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: 00:05:23 30139461 reads; of these: 30139461 (100.00%) were unpaired; of these: 11644620 (38.64%) aligned 0 times 14679643 (48.71%) aligned exactly 1 time 3815198 (12.66%) aligned >1 times 61.36% overall alignment rate Time searching: 00:05:23 Overall time: 00:05:23 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] 3330444 / 18494841 = 0.1801 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 @ Thu, 08 Oct 2020 22:07:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9008801/SRX9008801.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9008801/SRX9008801.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9008801/SRX9008801.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9008801/SRX9008801.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 @ Thu, 08 Oct 2020 22:07:40: #1 read tag files... INFO @ Thu, 08 Oct 2020 22:07:40: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 22:07:45: 1000000 INFO @ Thu, 08 Oct 2020 22:07:50: 2000000 INFO @ Thu, 08 Oct 2020 22:07:54: 3000000 INFO @ Thu, 08 Oct 2020 22:07:59: 4000000 INFO @ Thu, 08 Oct 2020 22:08:04: 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 @ Thu, 08 Oct 2020 22:08:08: 6000000 INFO @ Thu, 08 Oct 2020 22:08:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9008801/SRX9008801.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9008801/SRX9008801.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9008801/SRX9008801.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9008801/SRX9008801.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 @ Thu, 08 Oct 2020 22:08:11: #1 read tag files... INFO @ Thu, 08 Oct 2020 22:08:11: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 22:08:13: 7000000 INFO @ Thu, 08 Oct 2020 22:08:16: 1000000 INFO @ Thu, 08 Oct 2020 22:08:18: 8000000 INFO @ Thu, 08 Oct 2020 22:08:22: 2000000 INFO @ Thu, 08 Oct 2020 22:08:23: 9000000 INFO @ Thu, 08 Oct 2020 22:08:28: 3000000 INFO @ Thu, 08 Oct 2020 22:08:28: 10000000 INFO @ Thu, 08 Oct 2020 22:08:33: 11000000 INFO @ Thu, 08 Oct 2020 22:08:33: 4000000 INFO @ Thu, 08 Oct 2020 22:08:38: 12000000 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 @ Thu, 08 Oct 2020 22:08:39: 5000000 INFO @ Thu, 08 Oct 2020 22:08:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX9008801/SRX9008801.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX9008801/SRX9008801.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX9008801/SRX9008801.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX9008801/SRX9008801.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 @ Thu, 08 Oct 2020 22:08:41: #1 read tag files... INFO @ Thu, 08 Oct 2020 22:08:41: #1 read treatment tags... INFO @ Thu, 08 Oct 2020 22:08:43: 13000000 INFO @ Thu, 08 Oct 2020 22:08:44: 6000000 INFO @ Thu, 08 Oct 2020 22:08:46: 1000000 INFO @ Thu, 08 Oct 2020 22:08:48: 14000000 INFO @ Thu, 08 Oct 2020 22:08:50: 7000000 INFO @ Thu, 08 Oct 2020 22:08:51: 2000000 INFO @ Thu, 08 Oct 2020 22:08:53: 15000000 INFO @ Thu, 08 Oct 2020 22:08:54: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 22:08:54: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 22:08:54: #1 total tags in treatment: 15164397 INFO @ Thu, 08 Oct 2020 22:08:54: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 22:08:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 22:08:54: #1 tags after filtering in treatment: 15164393 INFO @ Thu, 08 Oct 2020 22:08:54: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 22:08:54: #1 finished! INFO @ Thu, 08 Oct 2020 22:08:54: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 22:08:54: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 22:08:55: 8000000 INFO @ Thu, 08 Oct 2020 22:08:56: #2 number of paired peaks: 598 WARNING @ Thu, 08 Oct 2020 22:08:56: Fewer paired peaks (598) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 598 pairs to build model! INFO @ Thu, 08 Oct 2020 22:08:56: start model_add_line... INFO @ Thu, 08 Oct 2020 22:08:56: start X-correlation... INFO @ Thu, 08 Oct 2020 22:08:56: 3000000 INFO @ Thu, 08 Oct 2020 22:08:56: end of X-cor INFO @ Thu, 08 Oct 2020 22:08:56: #2 finished! INFO @ Thu, 08 Oct 2020 22:08:56: #2 predicted fragment length is 42 bps INFO @ Thu, 08 Oct 2020 22:08:56: #2 alternative fragment length(s) may be 2,42 bps INFO @ Thu, 08 Oct 2020 22:08:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9008801/SRX9008801.05_model.r WARNING @ Thu, 08 Oct 2020 22:08:56: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 22:08:56: #2 You may need to consider one of the other alternative d(s): 2,42 WARNING @ Thu, 08 Oct 2020 22:08:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 22:08:56: #3 Call peaks... INFO @ Thu, 08 Oct 2020 22:08:56: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 22:09:01: 4000000 INFO @ Thu, 08 Oct 2020 22:09:01: 9000000 INFO @ Thu, 08 Oct 2020 22:09:05: 5000000 INFO @ Thu, 08 Oct 2020 22:09:06: 10000000 INFO @ Thu, 08 Oct 2020 22:09:10: 6000000 INFO @ Thu, 08 Oct 2020 22:09:12: 11000000 INFO @ Thu, 08 Oct 2020 22:09:15: 7000000 INFO @ Thu, 08 Oct 2020 22:09:17: 12000000 INFO @ Thu, 08 Oct 2020 22:09:20: 8000000 INFO @ Thu, 08 Oct 2020 22:09:23: 13000000 INFO @ Thu, 08 Oct 2020 22:09:24: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 22:09:25: 9000000 INFO @ Thu, 08 Oct 2020 22:09:29: 14000000 INFO @ Thu, 08 Oct 2020 22:09:30: 10000000 INFO @ Thu, 08 Oct 2020 22:09:34: 15000000 INFO @ Thu, 08 Oct 2020 22:09:35: 11000000 INFO @ Thu, 08 Oct 2020 22:09:36: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 22:09:36: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 22:09:36: #1 total tags in treatment: 15164397 INFO @ Thu, 08 Oct 2020 22:09:36: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 22:09:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 22:09:36: #1 tags after filtering in treatment: 15164393 INFO @ Thu, 08 Oct 2020 22:09:36: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 22:09:36: #1 finished! INFO @ Thu, 08 Oct 2020 22:09:36: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 22:09:36: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 22:09:37: #2 number of paired peaks: 598 WARNING @ Thu, 08 Oct 2020 22:09:37: Fewer paired peaks (598) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 598 pairs to build model! INFO @ Thu, 08 Oct 2020 22:09:37: start model_add_line... INFO @ Thu, 08 Oct 2020 22:09:37: start X-correlation... INFO @ Thu, 08 Oct 2020 22:09:37: end of X-cor INFO @ Thu, 08 Oct 2020 22:09:37: #2 finished! INFO @ Thu, 08 Oct 2020 22:09:37: #2 predicted fragment length is 42 bps INFO @ Thu, 08 Oct 2020 22:09:37: #2 alternative fragment length(s) may be 2,42 bps INFO @ Thu, 08 Oct 2020 22:09:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9008801/SRX9008801.10_model.r WARNING @ Thu, 08 Oct 2020 22:09:37: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 22:09:37: #2 You may need to consider one of the other alternative d(s): 2,42 WARNING @ Thu, 08 Oct 2020 22:09:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 22:09:37: #3 Call peaks... INFO @ Thu, 08 Oct 2020 22:09:37: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 22:09:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9008801/SRX9008801.05_peaks.xls INFO @ Thu, 08 Oct 2020 22:09:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9008801/SRX9008801.05_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 22:09:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9008801/SRX9008801.05_summits.bed INFO @ Thu, 08 Oct 2020 22:09:38: Done! pass1 - making usageList (524 chroms): 1 millis pass2 - checking and writing primary data (2028 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 22:09:39: 12000000 INFO @ Thu, 08 Oct 2020 22:09:44: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 08 Oct 2020 22:09:49: 14000000 INFO @ Thu, 08 Oct 2020 22:09:54: 15000000 INFO @ Thu, 08 Oct 2020 22:09:55: #1 tag size is determined as 50 bps INFO @ Thu, 08 Oct 2020 22:09:55: #1 tag size = 50 INFO @ Thu, 08 Oct 2020 22:09:55: #1 total tags in treatment: 15164397 INFO @ Thu, 08 Oct 2020 22:09:55: #1 user defined the maximum tags... INFO @ Thu, 08 Oct 2020 22:09:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 08 Oct 2020 22:09:55: #1 tags after filtering in treatment: 15164393 INFO @ Thu, 08 Oct 2020 22:09:55: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 08 Oct 2020 22:09:55: #1 finished! INFO @ Thu, 08 Oct 2020 22:09:55: #2 Build Peak Model... INFO @ Thu, 08 Oct 2020 22:09:55: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 08 Oct 2020 22:09:57: #2 number of paired peaks: 598 WARNING @ Thu, 08 Oct 2020 22:09:57: Fewer paired peaks (598) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 598 pairs to build model! INFO @ Thu, 08 Oct 2020 22:09:57: start model_add_line... INFO @ Thu, 08 Oct 2020 22:09:57: start X-correlation... INFO @ Thu, 08 Oct 2020 22:09:57: end of X-cor INFO @ Thu, 08 Oct 2020 22:09:57: #2 finished! INFO @ Thu, 08 Oct 2020 22:09:57: #2 predicted fragment length is 42 bps INFO @ Thu, 08 Oct 2020 22:09:57: #2 alternative fragment length(s) may be 2,42 bps INFO @ Thu, 08 Oct 2020 22:09:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX9008801/SRX9008801.20_model.r WARNING @ Thu, 08 Oct 2020 22:09:57: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 08 Oct 2020 22:09:57: #2 You may need to consider one of the other alternative d(s): 2,42 WARNING @ Thu, 08 Oct 2020 22:09:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 08 Oct 2020 22:09:57: #3 Call peaks... INFO @ Thu, 08 Oct 2020 22:09:57: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 08 Oct 2020 22:10:06: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Thu, 08 Oct 2020 22:10:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9008801/SRX9008801.10_peaks.xls INFO @ Thu, 08 Oct 2020 22:10:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9008801/SRX9008801.10_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 22:10:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9008801/SRX9008801.10_summits.bed INFO @ Thu, 08 Oct 2020 22:10:21: Done! pass1 - making usageList (445 chroms): 1 millis pass2 - checking and writing primary data (1738 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Thu, 08 Oct 2020 22:10:25: #3 Call peaks for each chromosome... INFO @ Thu, 08 Oct 2020 22:10:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX9008801/SRX9008801.20_peaks.xls INFO @ Thu, 08 Oct 2020 22:10:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX9008801/SRX9008801.20_peaks.narrowPeak INFO @ Thu, 08 Oct 2020 22:10:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX9008801/SRX9008801.20_summits.bed INFO @ Thu, 08 Oct 2020 22:10:39: Done! pass1 - making usageList (350 chroms): 1 millis pass2 - checking and writing primary data (948 records, 4 fields): 12 millis CompletedMACS2peakCalling