Job ID = 6455604 SRX = SRX287921 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:10:06 prefetch.2.10.7: 1) Downloading 'SRR870110'... 2020-06-21T10:10:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:13:09 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:13:09 prefetch.2.10.7: 1) 'SRR870110' was downloaded successfully Read 16164431 spots for SRR870110/SRR870110.sra Written 16164431 spots for SRR870110/SRR870110.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: 00:04:31 16164431 reads; of these: 16164431 (100.00%) were unpaired; of these: 1194613 (7.39%) aligned 0 times 11266113 (69.70%) aligned exactly 1 time 3703705 (22.91%) aligned >1 times 92.61% overall alignment rate Time searching: 00:04:31 Overall time: 00:04:31 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] 1685852 / 14969818 = 0.1126 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 19:22:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287921/SRX287921.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287921/SRX287921.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287921/SRX287921.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287921/SRX287921.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 19:22:39: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:22:39: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:22:45: 1000000 INFO @ Sun, 21 Jun 2020 19:22:51: 2000000 INFO @ Sun, 21 Jun 2020 19:22:57: 3000000 INFO @ Sun, 21 Jun 2020 19:23:02: 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 19:23:08: 5000000 INFO @ Sun, 21 Jun 2020 19:23:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287921/SRX287921.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287921/SRX287921.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287921/SRX287921.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287921/SRX287921.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 19:23:09: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:23:09: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:23:14: 6000000 INFO @ Sun, 21 Jun 2020 19:23:15: 1000000 INFO @ Sun, 21 Jun 2020 19:23:20: 7000000 INFO @ Sun, 21 Jun 2020 19:23:21: 2000000 INFO @ Sun, 21 Jun 2020 19:23:26: 8000000 INFO @ Sun, 21 Jun 2020 19:23:27: 3000000 INFO @ Sun, 21 Jun 2020 19:23:33: 9000000 INFO @ Sun, 21 Jun 2020 19:23:33: 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 19:23:39: 10000000 INFO @ Sun, 21 Jun 2020 19:23:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287921/SRX287921.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287921/SRX287921.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287921/SRX287921.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287921/SRX287921.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 19:23:39: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:23:39: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:23:40: 5000000 INFO @ Sun, 21 Jun 2020 19:23:46: 11000000 INFO @ Sun, 21 Jun 2020 19:23:46: 1000000 INFO @ Sun, 21 Jun 2020 19:23:47: 6000000 INFO @ Sun, 21 Jun 2020 19:23:53: 12000000 INFO @ Sun, 21 Jun 2020 19:23:54: 2000000 INFO @ Sun, 21 Jun 2020 19:23:54: 7000000 INFO @ Sun, 21 Jun 2020 19:24:01: 13000000 INFO @ Sun, 21 Jun 2020 19:24:01: 3000000 INFO @ Sun, 21 Jun 2020 19:24:01: 8000000 INFO @ Sun, 21 Jun 2020 19:24:03: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:24:03: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:24:03: #1 total tags in treatment: 13283966 INFO @ Sun, 21 Jun 2020 19:24:03: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:24:03: #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 19:24:03: #1 tags after filtering in treatment: 13283965 INFO @ Sun, 21 Jun 2020 19:24:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:24:03: #1 finished! INFO @ Sun, 21 Jun 2020 19:24:03: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:24:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:24:04: #2 number of paired peaks: 393 WARNING @ Sun, 21 Jun 2020 19:24:04: Fewer paired peaks (393) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 393 pairs to build model! INFO @ Sun, 21 Jun 2020 19:24:04: start model_add_line... INFO @ Sun, 21 Jun 2020 19:24:04: start X-correlation... INFO @ Sun, 21 Jun 2020 19:24:04: end of X-cor INFO @ Sun, 21 Jun 2020 19:24:04: #2 finished! INFO @ Sun, 21 Jun 2020 19:24:04: #2 predicted fragment length is 46 bps INFO @ Sun, 21 Jun 2020 19:24:04: #2 alternative fragment length(s) may be 4,46 bps INFO @ Sun, 21 Jun 2020 19:24:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287921/SRX287921.05_model.r WARNING @ Sun, 21 Jun 2020 19:24:04: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:24:04: #2 You may need to consider one of the other alternative d(s): 4,46 WARNING @ Sun, 21 Jun 2020 19:24:04: #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 19:24:04: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:24:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:24:08: 4000000 INFO @ Sun, 21 Jun 2020 19:24:08: 9000000 INFO @ Sun, 21 Jun 2020 19:24:15: 5000000 INFO @ Sun, 21 Jun 2020 19:24:16: 10000000 INFO @ Sun, 21 Jun 2020 19:24:22: 6000000 INFO @ Sun, 21 Jun 2020 19:24:23: 11000000 INFO @ Sun, 21 Jun 2020 19:24:30: 7000000 INFO @ Sun, 21 Jun 2020 19:24:31: 12000000 INFO @ Sun, 21 Jun 2020 19:24:31: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:24:37: 8000000 INFO @ Sun, 21 Jun 2020 19:24:38: 13000000 INFO @ Sun, 21 Jun 2020 19:24:40: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:24:40: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:24:40: #1 total tags in treatment: 13283966 INFO @ Sun, 21 Jun 2020 19:24:40: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:24:40: #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 19:24:41: #1 tags after filtering in treatment: 13283965 INFO @ Sun, 21 Jun 2020 19:24:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:24:41: #1 finished! INFO @ Sun, 21 Jun 2020 19:24:41: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:24:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:24:42: #2 number of paired peaks: 393 WARNING @ Sun, 21 Jun 2020 19:24:42: Fewer paired peaks (393) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 393 pairs to build model! INFO @ Sun, 21 Jun 2020 19:24:42: start model_add_line... INFO @ Sun, 21 Jun 2020 19:24:42: start X-correlation... INFO @ Sun, 21 Jun 2020 19:24:42: end of X-cor INFO @ Sun, 21 Jun 2020 19:24:42: #2 finished! INFO @ Sun, 21 Jun 2020 19:24:42: #2 predicted fragment length is 46 bps INFO @ Sun, 21 Jun 2020 19:24:42: #2 alternative fragment length(s) may be 4,46 bps INFO @ Sun, 21 Jun 2020 19:24:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287921/SRX287921.10_model.r WARNING @ Sun, 21 Jun 2020 19:24:42: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:24:42: #2 You may need to consider one of the other alternative d(s): 4,46 WARNING @ Sun, 21 Jun 2020 19:24:42: #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 19:24:42: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:24:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:24:43: 9000000 INFO @ Sun, 21 Jun 2020 19:24:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287921/SRX287921.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:24:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287921/SRX287921.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:24:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287921/SRX287921.05_summits.bed INFO @ Sun, 21 Jun 2020 19:24:44: Done! pass1 - making usageList (534 chroms): 1 millis pass2 - checking and writing primary data (2087 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:24:50: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:24:57: 11000000 INFO @ Sun, 21 Jun 2020 19:25:03: 12000000 INFO @ Sun, 21 Jun 2020 19:25:08: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:25:10: 13000000 INFO @ Sun, 21 Jun 2020 19:25:12: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:25:12: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:25:12: #1 total tags in treatment: 13283966 INFO @ Sun, 21 Jun 2020 19:25:12: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:25:12: #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 19:25:12: #1 tags after filtering in treatment: 13283965 INFO @ Sun, 21 Jun 2020 19:25:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:25:12: #1 finished! INFO @ Sun, 21 Jun 2020 19:25:12: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:25:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:25:13: #2 number of paired peaks: 393 WARNING @ Sun, 21 Jun 2020 19:25:13: Fewer paired peaks (393) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 393 pairs to build model! INFO @ Sun, 21 Jun 2020 19:25:13: start model_add_line... INFO @ Sun, 21 Jun 2020 19:25:13: start X-correlation... INFO @ Sun, 21 Jun 2020 19:25:13: end of X-cor INFO @ Sun, 21 Jun 2020 19:25:13: #2 finished! INFO @ Sun, 21 Jun 2020 19:25:13: #2 predicted fragment length is 46 bps INFO @ Sun, 21 Jun 2020 19:25:13: #2 alternative fragment length(s) may be 4,46 bps INFO @ Sun, 21 Jun 2020 19:25:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287921/SRX287921.20_model.r WARNING @ Sun, 21 Jun 2020 19:25:13: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:25:13: #2 You may need to consider one of the other alternative d(s): 4,46 WARNING @ Sun, 21 Jun 2020 19:25:13: #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 19:25:13: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:25:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:25:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287921/SRX287921.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:25:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287921/SRX287921.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:25:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287921/SRX287921.10_summits.bed INFO @ Sun, 21 Jun 2020 19:25:22: Done! pass1 - making usageList (451 chroms): 1 millis pass2 - checking and writing primary data (1551 records, 4 fields): 14 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:25:41: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:25:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287921/SRX287921.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:25:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287921/SRX287921.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:25:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287921/SRX287921.20_summits.bed INFO @ Sun, 21 Jun 2020 19:25:55: Done! pass1 - making usageList (256 chroms): 1 millis pass2 - checking and writing primary data (522 records, 4 fields): 9 millis CompletedMACS2peakCalling