Job ID = 6455651 SRX = SRX287959 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:24:36 prefetch.2.10.7: 1) Downloading 'SRR870148'... 2020-06-21T10:24:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:26:39 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:26:39 prefetch.2.10.7: 'SRR870148' is valid 2020-06-21T10:26:39 prefetch.2.10.7: 1) 'SRR870148' was downloaded successfully Read 13809114 spots for SRR870148/SRR870148.sra Written 13809114 spots for SRR870148/SRR870148.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: 00:04:11 13809114 reads; of these: 13809114 (100.00%) were unpaired; of these: 756665 (5.48%) aligned 0 times 9039824 (65.46%) aligned exactly 1 time 4012625 (29.06%) aligned >1 times 94.52% overall alignment rate Time searching: 00:04:11 Overall time: 00:04:11 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] 2216234 / 13052449 = 0.1698 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 19:35:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287959/SRX287959.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287959/SRX287959.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287959/SRX287959.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287959/SRX287959.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 19:35:05: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:35:05: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:35:13: 1000000 INFO @ Sun, 21 Jun 2020 19:35:20: 2000000 INFO @ Sun, 21 Jun 2020 19:35:27: 3000000 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 19:35:34: 4000000 INFO @ Sun, 21 Jun 2020 19:35:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287959/SRX287959.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287959/SRX287959.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287959/SRX287959.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287959/SRX287959.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 19:35:36: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:35:36: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:35:42: 5000000 INFO @ Sun, 21 Jun 2020 19:35:42: 1000000 INFO @ Sun, 21 Jun 2020 19:35:49: 2000000 INFO @ Sun, 21 Jun 2020 19:35:49: 6000000 INFO @ Sun, 21 Jun 2020 19:35:56: 3000000 INFO @ Sun, 21 Jun 2020 19:35:57: 7000000 INFO @ Sun, 21 Jun 2020 19:36:03: 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 19:36:05: 8000000 INFO @ Sun, 21 Jun 2020 19:36:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287959/SRX287959.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287959/SRX287959.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287959/SRX287959.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287959/SRX287959.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 19:36:05: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:36:05: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:36:09: 5000000 INFO @ Sun, 21 Jun 2020 19:36:13: 1000000 INFO @ Sun, 21 Jun 2020 19:36:14: 9000000 INFO @ Sun, 21 Jun 2020 19:36:16: 6000000 INFO @ Sun, 21 Jun 2020 19:36:20: 2000000 INFO @ Sun, 21 Jun 2020 19:36:22: 10000000 INFO @ Sun, 21 Jun 2020 19:36:23: 7000000 INFO @ Sun, 21 Jun 2020 19:36:27: 3000000 INFO @ Sun, 21 Jun 2020 19:36:28: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:36:28: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:36:28: #1 total tags in treatment: 10836215 INFO @ Sun, 21 Jun 2020 19:36:28: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:36:28: #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 19:36:29: #1 tags after filtering in treatment: 10836215 INFO @ Sun, 21 Jun 2020 19:36:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:36:29: #1 finished! INFO @ Sun, 21 Jun 2020 19:36:29: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:36:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:36:30: #2 number of paired peaks: 721 WARNING @ Sun, 21 Jun 2020 19:36:30: Fewer paired peaks (721) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 721 pairs to build model! INFO @ Sun, 21 Jun 2020 19:36:30: start model_add_line... INFO @ Sun, 21 Jun 2020 19:36:30: start X-correlation... INFO @ Sun, 21 Jun 2020 19:36:30: end of X-cor INFO @ Sun, 21 Jun 2020 19:36:30: #2 finished! INFO @ Sun, 21 Jun 2020 19:36:30: #2 predicted fragment length is 46 bps INFO @ Sun, 21 Jun 2020 19:36:30: #2 alternative fragment length(s) may be 4,46 bps INFO @ Sun, 21 Jun 2020 19:36:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287959/SRX287959.05_model.r WARNING @ Sun, 21 Jun 2020 19:36:30: #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 19:36:30: #2 You may need to consider one of the other alternative d(s): 4,46 WARNING @ Sun, 21 Jun 2020 19:36:30: #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 19:36:30: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:36:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:36:30: 8000000 INFO @ Sun, 21 Jun 2020 19:36:34: 4000000 INFO @ Sun, 21 Jun 2020 19:36:37: 9000000 INFO @ Sun, 21 Jun 2020 19:36:40: 5000000 INFO @ Sun, 21 Jun 2020 19:36:43: 10000000 INFO @ Sun, 21 Jun 2020 19:36:47: 6000000 INFO @ Sun, 21 Jun 2020 19:36:49: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:36:49: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:36:49: #1 total tags in treatment: 10836215 INFO @ Sun, 21 Jun 2020 19:36:49: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:36:49: #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 19:36:49: #1 tags after filtering in treatment: 10836215 INFO @ Sun, 21 Jun 2020 19:36:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:36:49: #1 finished! INFO @ Sun, 21 Jun 2020 19:36:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:36:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:36:50: #2 number of paired peaks: 721 WARNING @ Sun, 21 Jun 2020 19:36:50: Fewer paired peaks (721) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 721 pairs to build model! INFO @ Sun, 21 Jun 2020 19:36:50: start model_add_line... INFO @ Sun, 21 Jun 2020 19:36:50: start X-correlation... INFO @ Sun, 21 Jun 2020 19:36:50: end of X-cor INFO @ Sun, 21 Jun 2020 19:36:50: #2 finished! INFO @ Sun, 21 Jun 2020 19:36:50: #2 predicted fragment length is 46 bps INFO @ Sun, 21 Jun 2020 19:36:50: #2 alternative fragment length(s) may be 4,46 bps INFO @ Sun, 21 Jun 2020 19:36:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287959/SRX287959.10_model.r WARNING @ Sun, 21 Jun 2020 19:36:50: #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 19:36:50: #2 You may need to consider one of the other alternative d(s): 4,46 WARNING @ Sun, 21 Jun 2020 19:36:50: #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 19:36:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:36:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:36:51: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:36:53: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:36:59: 8000000 INFO @ Sun, 21 Jun 2020 19:37:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287959/SRX287959.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:37:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287959/SRX287959.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:37:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287959/SRX287959.05_summits.bed INFO @ Sun, 21 Jun 2020 19:37:02: Done! pass1 - making usageList (579 chroms): 1 millis pass2 - checking and writing primary data (2201 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:37:05: 9000000 INFO @ Sun, 21 Jun 2020 19:37:11: 10000000 INFO @ Sun, 21 Jun 2020 19:37:12: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:37:15: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:37:15: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:37:15: #1 total tags in treatment: 10836215 INFO @ Sun, 21 Jun 2020 19:37:15: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:37:15: #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 19:37:16: #1 tags after filtering in treatment: 10836215 INFO @ Sun, 21 Jun 2020 19:37:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:37:16: #1 finished! INFO @ Sun, 21 Jun 2020 19:37:16: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:37:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:37:17: #2 number of paired peaks: 721 WARNING @ Sun, 21 Jun 2020 19:37:17: Fewer paired peaks (721) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 721 pairs to build model! INFO @ Sun, 21 Jun 2020 19:37:17: start model_add_line... INFO @ Sun, 21 Jun 2020 19:37:17: start X-correlation... INFO @ Sun, 21 Jun 2020 19:37:17: end of X-cor INFO @ Sun, 21 Jun 2020 19:37:17: #2 finished! INFO @ Sun, 21 Jun 2020 19:37:17: #2 predicted fragment length is 46 bps INFO @ Sun, 21 Jun 2020 19:37:17: #2 alternative fragment length(s) may be 4,46 bps INFO @ Sun, 21 Jun 2020 19:37:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287959/SRX287959.20_model.r WARNING @ Sun, 21 Jun 2020 19:37:17: #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 19:37:17: #2 You may need to consider one of the other alternative d(s): 4,46 WARNING @ Sun, 21 Jun 2020 19:37:17: #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 19:37:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:37:17: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:37:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287959/SRX287959.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:37:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287959/SRX287959.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:37:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287959/SRX287959.10_summits.bed INFO @ Sun, 21 Jun 2020 19:37:22: Done! pass1 - making usageList (496 chroms): 1 millis pass2 - checking and writing primary data (1807 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:37:38: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:37:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287959/SRX287959.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:37:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287959/SRX287959.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:37:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287959/SRX287959.20_summits.bed INFO @ Sun, 21 Jun 2020 19:37:49: Done! pass1 - making usageList (326 chroms): 1 millis pass2 - checking and writing primary data (722 records, 4 fields): 10 millis CompletedMACS2peakCalling