Job ID = 6459229 SRX = SRX645140 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:55:52 prefetch.2.10.7: 1) Downloading 'SRR1505740'... 2020-06-21T12:55:52 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:01:53 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:01:53 prefetch.2.10.7: 1) 'SRR1505740' was downloaded successfully Read 20492134 spots for SRR1505740/SRR1505740.sra Written 20492134 spots for SRR1505740/SRR1505740.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: 00:08:46 20492134 reads; of these: 20492134 (100.00%) were unpaired; of these: 9633062 (47.01%) aligned 0 times 7781703 (37.97%) aligned exactly 1 time 3077369 (15.02%) aligned >1 times 52.99% overall alignment rate Time searching: 00:08:46 Overall time: 00:08:46 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] 1126772 / 10859072 = 0.1038 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 22:16:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX645140/SRX645140.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX645140/SRX645140.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX645140/SRX645140.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX645140/SRX645140.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 22:16:45: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:16:45: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:16:52: 1000000 INFO @ Sun, 21 Jun 2020 22:16:58: 2000000 INFO @ Sun, 21 Jun 2020 22:17:05: 3000000 INFO @ Sun, 21 Jun 2020 22:17:12: 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 22:17:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX645140/SRX645140.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX645140/SRX645140.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX645140/SRX645140.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX645140/SRX645140.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 22:17:15: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:17:15: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:17:19: 5000000 INFO @ Sun, 21 Jun 2020 22:17:23: 1000000 INFO @ Sun, 21 Jun 2020 22:17:26: 6000000 INFO @ Sun, 21 Jun 2020 22:17:30: 2000000 INFO @ Sun, 21 Jun 2020 22:17:33: 7000000 INFO @ Sun, 21 Jun 2020 22:17:37: 3000000 INFO @ Sun, 21 Jun 2020 22:17:41: 8000000 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 22:17:45: 4000000 INFO @ Sun, 21 Jun 2020 22:17:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX645140/SRX645140.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX645140/SRX645140.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX645140/SRX645140.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX645140/SRX645140.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 22:17:45: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:17:45: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:17:49: 9000000 INFO @ Sun, 21 Jun 2020 22:17:52: 5000000 INFO @ Sun, 21 Jun 2020 22:17:53: 1000000 INFO @ Sun, 21 Jun 2020 22:17:54: #1 tag size is determined as 100 bps INFO @ Sun, 21 Jun 2020 22:17:54: #1 tag size = 100 INFO @ Sun, 21 Jun 2020 22:17:54: #1 total tags in treatment: 9732300 INFO @ Sun, 21 Jun 2020 22:17:54: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:17:54: #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 22:17:55: #1 tags after filtering in treatment: 9732293 INFO @ Sun, 21 Jun 2020 22:17:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:17:55: #1 finished! INFO @ Sun, 21 Jun 2020 22:17:55: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:17:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:17:55: #2 number of paired peaks: 657 WARNING @ Sun, 21 Jun 2020 22:17:55: Fewer paired peaks (657) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 657 pairs to build model! INFO @ Sun, 21 Jun 2020 22:17:55: start model_add_line... INFO @ Sun, 21 Jun 2020 22:17:55: start X-correlation... INFO @ Sun, 21 Jun 2020 22:17:55: end of X-cor INFO @ Sun, 21 Jun 2020 22:17:55: #2 finished! INFO @ Sun, 21 Jun 2020 22:17:55: #2 predicted fragment length is 92 bps INFO @ Sun, 21 Jun 2020 22:17:55: #2 alternative fragment length(s) may be 92 bps INFO @ Sun, 21 Jun 2020 22:17:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX645140/SRX645140.05_model.r WARNING @ Sun, 21 Jun 2020 22:17:55: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:17:55: #2 You may need to consider one of the other alternative d(s): 92 WARNING @ Sun, 21 Jun 2020 22:17:55: #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 22:17:55: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:17:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:17:59: 6000000 INFO @ Sun, 21 Jun 2020 22:18:00: 2000000 INFO @ Sun, 21 Jun 2020 22:18:07: 7000000 INFO @ Sun, 21 Jun 2020 22:18:07: 3000000 INFO @ Sun, 21 Jun 2020 22:18:14: 8000000 INFO @ Sun, 21 Jun 2020 22:18:15: 4000000 INFO @ Sun, 21 Jun 2020 22:18:16: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:18:22: 9000000 INFO @ Sun, 21 Jun 2020 22:18:22: 5000000 INFO @ Sun, 21 Jun 2020 22:18:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX645140/SRX645140.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:18:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX645140/SRX645140.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:18:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX645140/SRX645140.05_summits.bed INFO @ Sun, 21 Jun 2020 22:18:25: Done! pass1 - making usageList (731 chroms): 1 millis pass2 - checking and writing primary data (2097 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:18:27: #1 tag size is determined as 100 bps INFO @ Sun, 21 Jun 2020 22:18:27: #1 tag size = 100 INFO @ Sun, 21 Jun 2020 22:18:27: #1 total tags in treatment: 9732300 INFO @ Sun, 21 Jun 2020 22:18:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:18:27: #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 22:18:28: #1 tags after filtering in treatment: 9732293 INFO @ Sun, 21 Jun 2020 22:18:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:18:28: #1 finished! INFO @ Sun, 21 Jun 2020 22:18:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:18:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:18:28: #2 number of paired peaks: 657 WARNING @ Sun, 21 Jun 2020 22:18:28: Fewer paired peaks (657) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 657 pairs to build model! INFO @ Sun, 21 Jun 2020 22:18:28: start model_add_line... INFO @ Sun, 21 Jun 2020 22:18:28: start X-correlation... INFO @ Sun, 21 Jun 2020 22:18:28: end of X-cor INFO @ Sun, 21 Jun 2020 22:18:28: #2 finished! INFO @ Sun, 21 Jun 2020 22:18:28: #2 predicted fragment length is 92 bps INFO @ Sun, 21 Jun 2020 22:18:28: #2 alternative fragment length(s) may be 92 bps INFO @ Sun, 21 Jun 2020 22:18:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX645140/SRX645140.10_model.r WARNING @ Sun, 21 Jun 2020 22:18:28: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:18:28: #2 You may need to consider one of the other alternative d(s): 92 WARNING @ Sun, 21 Jun 2020 22:18:28: #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 22:18:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:18:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:18:29: 6000000 INFO @ Sun, 21 Jun 2020 22:18:36: 7000000 INFO @ Sun, 21 Jun 2020 22:18:43: 8000000 INFO @ Sun, 21 Jun 2020 22:18:49: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:18:50: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:18:56: #1 tag size is determined as 100 bps INFO @ Sun, 21 Jun 2020 22:18:56: #1 tag size = 100 INFO @ Sun, 21 Jun 2020 22:18:56: #1 total tags in treatment: 9732300 INFO @ Sun, 21 Jun 2020 22:18:56: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:18:56: #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 22:18:56: #1 tags after filtering in treatment: 9732293 INFO @ Sun, 21 Jun 2020 22:18:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:18:56: #1 finished! INFO @ Sun, 21 Jun 2020 22:18:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:18:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:18:57: #2 number of paired peaks: 657 WARNING @ Sun, 21 Jun 2020 22:18:57: Fewer paired peaks (657) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 657 pairs to build model! INFO @ Sun, 21 Jun 2020 22:18:57: start model_add_line... INFO @ Sun, 21 Jun 2020 22:18:57: start X-correlation... INFO @ Sun, 21 Jun 2020 22:18:57: end of X-cor INFO @ Sun, 21 Jun 2020 22:18:57: #2 finished! INFO @ Sun, 21 Jun 2020 22:18:57: #2 predicted fragment length is 92 bps INFO @ Sun, 21 Jun 2020 22:18:57: #2 alternative fragment length(s) may be 92 bps INFO @ Sun, 21 Jun 2020 22:18:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX645140/SRX645140.20_model.r WARNING @ Sun, 21 Jun 2020 22:18:57: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:18:57: #2 You may need to consider one of the other alternative d(s): 92 WARNING @ Sun, 21 Jun 2020 22:18:57: #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 22:18:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:18:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:18:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX645140/SRX645140.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:18:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX645140/SRX645140.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:18:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX645140/SRX645140.10_summits.bed INFO @ Sun, 21 Jun 2020 22:18:58: Done! pass1 - making usageList (623 chroms): 1 millis pass2 - checking and writing primary data (1521 records, 4 fields): 17 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:19:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:19:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX645140/SRX645140.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:19:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX645140/SRX645140.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:19:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX645140/SRX645140.20_summits.bed INFO @ Sun, 21 Jun 2020 22:19:26: Done! pass1 - making usageList (475 chroms): 1 millis pass2 - checking and writing primary data (889 records, 4 fields): 13 millis CompletedMACS2peakCalling