Job ID = 6455609 SRX = SRX287925 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:07:51 prefetch.2.10.7: 1) Downloading 'SRR870114'... 2020-06-21T10:07:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:10:50 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:10:50 prefetch.2.10.7: 1) 'SRR870114' was downloaded successfully Read 21266404 spots for SRR870114/SRR870114.sra Written 21266404 spots for SRR870114/SRR870114.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: 00:05:58 21266404 reads; of these: 21266404 (100.00%) were unpaired; of these: 1611529 (7.58%) aligned 0 times 13447272 (63.23%) aligned exactly 1 time 6207603 (29.19%) aligned >1 times 92.42% overall alignment rate Time searching: 00:05:58 Overall time: 00:05:58 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 12 files... [bam_rmdupse_core] 4582201 / 19654875 = 0.2331 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 19:22:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287925/SRX287925.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287925/SRX287925.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287925/SRX287925.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287925/SRX287925.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 19:22:43: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:22:43: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:22:50: 1000000 INFO @ Sun, 21 Jun 2020 19:22:56: 2000000 INFO @ Sun, 21 Jun 2020 19:23:02: 3000000 INFO @ Sun, 21 Jun 2020 19:23:09: 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 19:23:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287925/SRX287925.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287925/SRX287925.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287925/SRX287925.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287925/SRX287925.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 19:23:13: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:23:13: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:23:15: 5000000 INFO @ Sun, 21 Jun 2020 19:23:20: 1000000 INFO @ Sun, 21 Jun 2020 19:23:22: 6000000 INFO @ Sun, 21 Jun 2020 19:23:27: 2000000 INFO @ Sun, 21 Jun 2020 19:23:29: 7000000 INFO @ Sun, 21 Jun 2020 19:23:34: 3000000 INFO @ Sun, 21 Jun 2020 19:23:35: 8000000 INFO @ Sun, 21 Jun 2020 19:23:41: 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 19:23:42: 9000000 INFO @ Sun, 21 Jun 2020 19:23:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287925/SRX287925.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287925/SRX287925.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287925/SRX287925.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287925/SRX287925.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 19:23:43: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:23:43: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:23:47: 5000000 INFO @ Sun, 21 Jun 2020 19:23:49: 10000000 INFO @ Sun, 21 Jun 2020 19:23:50: 1000000 INFO @ Sun, 21 Jun 2020 19:23:54: 6000000 INFO @ Sun, 21 Jun 2020 19:23:56: 11000000 INFO @ Sun, 21 Jun 2020 19:23:57: 2000000 INFO @ Sun, 21 Jun 2020 19:24:01: 7000000 INFO @ Sun, 21 Jun 2020 19:24:04: 12000000 INFO @ Sun, 21 Jun 2020 19:24:05: 3000000 INFO @ Sun, 21 Jun 2020 19:24:09: 8000000 INFO @ Sun, 21 Jun 2020 19:24:12: 13000000 INFO @ Sun, 21 Jun 2020 19:24:12: 4000000 INFO @ Sun, 21 Jun 2020 19:24:16: 9000000 INFO @ Sun, 21 Jun 2020 19:24:19: 14000000 INFO @ Sun, 21 Jun 2020 19:24:19: 5000000 INFO @ Sun, 21 Jun 2020 19:24:24: 10000000 INFO @ Sun, 21 Jun 2020 19:24:26: 6000000 INFO @ Sun, 21 Jun 2020 19:24:26: 15000000 INFO @ Sun, 21 Jun 2020 19:24:27: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:24:27: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:24:27: #1 total tags in treatment: 15072674 INFO @ Sun, 21 Jun 2020 19:24:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:24:27: #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 19:24:27: #1 tags after filtering in treatment: 15072674 INFO @ Sun, 21 Jun 2020 19:24:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:24:27: #1 finished! INFO @ Sun, 21 Jun 2020 19:24:27: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:24:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:24:29: #2 number of paired peaks: 740 WARNING @ Sun, 21 Jun 2020 19:24:29: Fewer paired peaks (740) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 740 pairs to build model! INFO @ Sun, 21 Jun 2020 19:24:29: start model_add_line... INFO @ Sun, 21 Jun 2020 19:24:29: start X-correlation... INFO @ Sun, 21 Jun 2020 19:24:29: end of X-cor INFO @ Sun, 21 Jun 2020 19:24:29: #2 finished! INFO @ Sun, 21 Jun 2020 19:24:29: #2 predicted fragment length is 35 bps INFO @ Sun, 21 Jun 2020 19:24:29: #2 alternative fragment length(s) may be 3,35 bps INFO @ Sun, 21 Jun 2020 19:24:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287925/SRX287925.05_model.r WARNING @ Sun, 21 Jun 2020 19:24:29: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:24:29: #2 You may need to consider one of the other alternative d(s): 3,35 WARNING @ Sun, 21 Jun 2020 19:24:29: #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 19:24:29: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:24:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:24:31: 11000000 INFO @ Sun, 21 Jun 2020 19:24:33: 7000000 INFO @ Sun, 21 Jun 2020 19:24:38: 12000000 INFO @ Sun, 21 Jun 2020 19:24:40: 8000000 INFO @ Sun, 21 Jun 2020 19:24:46: 13000000 INFO @ Sun, 21 Jun 2020 19:24:47: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:24:53: 14000000 INFO @ Sun, 21 Jun 2020 19:24:55: 10000000 INFO @ Sun, 21 Jun 2020 19:24:58: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:25:00: 15000000 INFO @ Sun, 21 Jun 2020 19:25:01: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:25:01: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:25:01: #1 total tags in treatment: 15072674 INFO @ Sun, 21 Jun 2020 19:25:01: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:25:01: #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 19:25:01: #1 tags after filtering in treatment: 15072674 INFO @ Sun, 21 Jun 2020 19:25:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:25:01: #1 finished! INFO @ Sun, 21 Jun 2020 19:25:01: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:25:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:25:02: 11000000 INFO @ Sun, 21 Jun 2020 19:25:02: #2 number of paired peaks: 740 WARNING @ Sun, 21 Jun 2020 19:25:02: Fewer paired peaks (740) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 740 pairs to build model! INFO @ Sun, 21 Jun 2020 19:25:02: start model_add_line... INFO @ Sun, 21 Jun 2020 19:25:02: start X-correlation... INFO @ Sun, 21 Jun 2020 19:25:02: end of X-cor INFO @ Sun, 21 Jun 2020 19:25:02: #2 finished! INFO @ Sun, 21 Jun 2020 19:25:02: #2 predicted fragment length is 35 bps INFO @ Sun, 21 Jun 2020 19:25:02: #2 alternative fragment length(s) may be 3,35 bps INFO @ Sun, 21 Jun 2020 19:25:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287925/SRX287925.10_model.r WARNING @ Sun, 21 Jun 2020 19:25:02: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:25:02: #2 You may need to consider one of the other alternative d(s): 3,35 WARNING @ Sun, 21 Jun 2020 19:25:02: #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 19:25:02: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:25:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:25:08: 12000000 INFO @ Sun, 21 Jun 2020 19:25:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287925/SRX287925.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:25:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287925/SRX287925.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:25:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287925/SRX287925.05_summits.bed INFO @ Sun, 21 Jun 2020 19:25:12: Done! pass1 - making usageList (636 chroms): 1 millis pass2 - checking and writing primary data (2407 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:25:15: 13000000 INFO @ Sun, 21 Jun 2020 19:25:21: 14000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:25:28: 15000000 INFO @ Sun, 21 Jun 2020 19:25:28: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:25:28: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:25:28: #1 total tags in treatment: 15072674 INFO @ Sun, 21 Jun 2020 19:25:28: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:25:28: #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 19:25:29: #1 tags after filtering in treatment: 15072674 INFO @ Sun, 21 Jun 2020 19:25:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:25:29: #1 finished! INFO @ Sun, 21 Jun 2020 19:25:29: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:25:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:25:30: #2 number of paired peaks: 740 WARNING @ Sun, 21 Jun 2020 19:25:30: Fewer paired peaks (740) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 740 pairs to build model! INFO @ Sun, 21 Jun 2020 19:25:30: start model_add_line... INFO @ Sun, 21 Jun 2020 19:25:30: start X-correlation... INFO @ Sun, 21 Jun 2020 19:25:30: end of X-cor INFO @ Sun, 21 Jun 2020 19:25:30: #2 finished! INFO @ Sun, 21 Jun 2020 19:25:30: #2 predicted fragment length is 35 bps INFO @ Sun, 21 Jun 2020 19:25:30: #2 alternative fragment length(s) may be 3,35 bps INFO @ Sun, 21 Jun 2020 19:25:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287925/SRX287925.20_model.r WARNING @ Sun, 21 Jun 2020 19:25:30: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:25:30: #2 You may need to consider one of the other alternative d(s): 3,35 WARNING @ Sun, 21 Jun 2020 19:25:30: #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 19:25:30: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:25:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:25:30: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:25:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287925/SRX287925.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:25:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287925/SRX287925.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:25:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287925/SRX287925.10_summits.bed INFO @ Sun, 21 Jun 2020 19:25:44: Done! pass1 - making usageList (505 chroms): 1 millis pass2 - checking and writing primary data (1997 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:25:58: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:26:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287925/SRX287925.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:26:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287925/SRX287925.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:26:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287925/SRX287925.20_summits.bed INFO @ Sun, 21 Jun 2020 19:26:11: Done! pass1 - making usageList (344 chroms): 1 millis pass2 - checking and writing primary data (792 records, 4 fields): 11 millis CompletedMACS2peakCalling