Job ID = 6456162 SRX = SRX3270985 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:39:38 prefetch.2.10.7: 1) Downloading 'SRR6159396'... 2020-06-21T10:39:38 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:44:37 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:44:37 prefetch.2.10.7: 1) 'SRR6159396' was downloaded successfully Read 24159113 spots for SRR6159396/SRR6159396.sra Written 24159113 spots for SRR6159396/SRR6159396.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: 00:05:39 24159113 reads; of these: 24159113 (100.00%) were unpaired; of these: 2156334 (8.93%) aligned 0 times 15930123 (65.94%) aligned exactly 1 time 6072656 (25.14%) aligned >1 times 91.07% overall alignment rate Time searching: 00:05:39 Overall time: 00:05:39 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] 9910008 / 22002779 = 0.4504 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 19:55:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3270985/SRX3270985.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3270985/SRX3270985.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3270985/SRX3270985.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3270985/SRX3270985.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 19:55:42: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:55:42: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:55:46: 1000000 INFO @ Sun, 21 Jun 2020 19:55:51: 2000000 INFO @ Sun, 21 Jun 2020 19:55:56: 3000000 INFO @ Sun, 21 Jun 2020 19:56:00: 4000000 INFO @ Sun, 21 Jun 2020 19:56:05: 5000000 INFO @ Sun, 21 Jun 2020 19:56:09: 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 @ Sun, 21 Jun 2020 19:56:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3270985/SRX3270985.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3270985/SRX3270985.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3270985/SRX3270985.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3270985/SRX3270985.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 19:56:12: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:56:12: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:56:14: 7000000 INFO @ Sun, 21 Jun 2020 19:56:17: 1000000 INFO @ Sun, 21 Jun 2020 19:56:19: 8000000 INFO @ Sun, 21 Jun 2020 19:56:22: 2000000 INFO @ Sun, 21 Jun 2020 19:56:24: 9000000 INFO @ Sun, 21 Jun 2020 19:56:27: 3000000 INFO @ Sun, 21 Jun 2020 19:56:29: 10000000 INFO @ Sun, 21 Jun 2020 19:56:32: 4000000 INFO @ Sun, 21 Jun 2020 19:56:33: 11000000 INFO @ Sun, 21 Jun 2020 19:56:38: 5000000 INFO @ Sun, 21 Jun 2020 19:56:38: 12000000 INFO @ Sun, 21 Jun 2020 19:56:39: #1 tag size is determined as 45 bps INFO @ Sun, 21 Jun 2020 19:56:39: #1 tag size = 45 INFO @ Sun, 21 Jun 2020 19:56:39: #1 total tags in treatment: 12092771 INFO @ Sun, 21 Jun 2020 19:56:39: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:56:39: #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 19:56:39: #1 tags after filtering in treatment: 12092771 INFO @ Sun, 21 Jun 2020 19:56:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:56:39: #1 finished! INFO @ Sun, 21 Jun 2020 19:56:39: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:56:39: #2 looking for paired plus/minus strand peaks... 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 19:56:40: #2 number of paired peaks: 1065 INFO @ Sun, 21 Jun 2020 19:56:40: start model_add_line... INFO @ Sun, 21 Jun 2020 19:56:40: start X-correlation... INFO @ Sun, 21 Jun 2020 19:56:40: end of X-cor INFO @ Sun, 21 Jun 2020 19:56:40: #2 finished! INFO @ Sun, 21 Jun 2020 19:56:40: #2 predicted fragment length is 42 bps INFO @ Sun, 21 Jun 2020 19:56:40: #2 alternative fragment length(s) may be 2,42 bps INFO @ Sun, 21 Jun 2020 19:56:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3270985/SRX3270985.05_model.r WARNING @ Sun, 21 Jun 2020 19:56:40: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:56:40: #2 You may need to consider one of the other alternative d(s): 2,42 WARNING @ Sun, 21 Jun 2020 19:56:40: #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 19:56:40: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:56:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:56:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3270985/SRX3270985.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3270985/SRX3270985.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3270985/SRX3270985.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3270985/SRX3270985.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 19:56:42: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:56:42: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:56:43: 6000000 INFO @ Sun, 21 Jun 2020 19:56:47: 1000000 INFO @ Sun, 21 Jun 2020 19:56:48: 7000000 INFO @ Sun, 21 Jun 2020 19:56:52: 2000000 INFO @ Sun, 21 Jun 2020 19:56:54: 8000000 INFO @ Sun, 21 Jun 2020 19:56:58: 3000000 INFO @ Sun, 21 Jun 2020 19:56:59: 9000000 INFO @ Sun, 21 Jun 2020 19:57:03: 4000000 INFO @ Sun, 21 Jun 2020 19:57:04: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:57:05: 10000000 INFO @ Sun, 21 Jun 2020 19:57:08: 5000000 INFO @ Sun, 21 Jun 2020 19:57:10: 11000000 INFO @ Sun, 21 Jun 2020 19:57:14: 6000000 INFO @ Sun, 21 Jun 2020 19:57:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3270985/SRX3270985.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:57:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3270985/SRX3270985.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:57:15: 12000000 INFO @ Sun, 21 Jun 2020 19:57:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3270985/SRX3270985.05_summits.bed INFO @ Sun, 21 Jun 2020 19:57:15: Done! pass1 - making usageList (654 chroms): 1 millis pass2 - checking and writing primary data (2624 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:57:16: #1 tag size is determined as 45 bps INFO @ Sun, 21 Jun 2020 19:57:16: #1 tag size = 45 INFO @ Sun, 21 Jun 2020 19:57:16: #1 total tags in treatment: 12092771 INFO @ Sun, 21 Jun 2020 19:57:16: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:57:16: #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 19:57:16: #1 tags after filtering in treatment: 12092771 INFO @ Sun, 21 Jun 2020 19:57:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:57:16: #1 finished! INFO @ Sun, 21 Jun 2020 19:57:16: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:57:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:57:17: #2 number of paired peaks: 1065 INFO @ Sun, 21 Jun 2020 19:57:17: start model_add_line... INFO @ Sun, 21 Jun 2020 19:57:17: start X-correlation... INFO @ Sun, 21 Jun 2020 19:57:17: end of X-cor INFO @ Sun, 21 Jun 2020 19:57:17: #2 finished! INFO @ Sun, 21 Jun 2020 19:57:17: #2 predicted fragment length is 42 bps INFO @ Sun, 21 Jun 2020 19:57:17: #2 alternative fragment length(s) may be 2,42 bps INFO @ Sun, 21 Jun 2020 19:57:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3270985/SRX3270985.10_model.r WARNING @ Sun, 21 Jun 2020 19:57:17: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:57:17: #2 You may need to consider one of the other alternative d(s): 2,42 WARNING @ Sun, 21 Jun 2020 19:57:17: #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 19:57:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:57:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:57:19: 7000000 INFO @ Sun, 21 Jun 2020 19:57:24: 8000000 INFO @ Sun, 21 Jun 2020 19:57:30: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:57:36: 10000000 INFO @ Sun, 21 Jun 2020 19:57:40: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:57:41: 11000000 INFO @ Sun, 21 Jun 2020 19:57:47: 12000000 INFO @ Sun, 21 Jun 2020 19:57:47: #1 tag size is determined as 45 bps INFO @ Sun, 21 Jun 2020 19:57:47: #1 tag size = 45 INFO @ Sun, 21 Jun 2020 19:57:47: #1 total tags in treatment: 12092771 INFO @ Sun, 21 Jun 2020 19:57:47: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:57:47: #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 19:57:48: #1 tags after filtering in treatment: 12092771 INFO @ Sun, 21 Jun 2020 19:57:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:57:48: #1 finished! INFO @ Sun, 21 Jun 2020 19:57:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:57:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:57:48: #2 number of paired peaks: 1065 INFO @ Sun, 21 Jun 2020 19:57:48: start model_add_line... INFO @ Sun, 21 Jun 2020 19:57:49: start X-correlation... INFO @ Sun, 21 Jun 2020 19:57:49: end of X-cor INFO @ Sun, 21 Jun 2020 19:57:49: #2 finished! INFO @ Sun, 21 Jun 2020 19:57:49: #2 predicted fragment length is 42 bps INFO @ Sun, 21 Jun 2020 19:57:49: #2 alternative fragment length(s) may be 2,42 bps INFO @ Sun, 21 Jun 2020 19:57:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3270985/SRX3270985.20_model.r WARNING @ Sun, 21 Jun 2020 19:57:49: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:57:49: #2 You may need to consider one of the other alternative d(s): 2,42 WARNING @ Sun, 21 Jun 2020 19:57:49: #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 19:57:49: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:57:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:57:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3270985/SRX3270985.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:57:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3270985/SRX3270985.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:57:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3270985/SRX3270985.10_summits.bed INFO @ Sun, 21 Jun 2020 19:57:52: Done! pass1 - making usageList (523 chroms): 1 millis pass2 - checking and writing primary data (2109 records, 4 fields): 15 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:58:12: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:58:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3270985/SRX3270985.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:58:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3270985/SRX3270985.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:58:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3270985/SRX3270985.20_summits.bed INFO @ Sun, 21 Jun 2020 19:58:24: Done! pass1 - making usageList (404 chroms): 1 millis pass2 - checking and writing primary data (1310 records, 4 fields): 12 millis CompletedMACS2peakCalling