Job ID = 6455493 SRX = SRX287830 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:21:21 prefetch.2.10.7: 1) Downloading 'SRR870019'... 2020-06-21T10:21:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:24:23 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:24:23 prefetch.2.10.7: 1) 'SRR870019' was downloaded successfully Read 17133552 spots for SRR870019/SRR870019.sra Written 17133552 spots for SRR870019/SRR870019.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: 00:05:05 17133552 reads; of these: 17133552 (100.00%) were unpaired; of these: 963615 (5.62%) aligned 0 times 11195678 (65.34%) aligned exactly 1 time 4974259 (29.03%) aligned >1 times 94.38% overall alignment rate Time searching: 00:05:05 Overall time: 00:05:05 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] 2735455 / 16169937 = 0.1692 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 19:34:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287830/SRX287830.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287830/SRX287830.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287830/SRX287830.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287830/SRX287830.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 19:34:21: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:34:21: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:34:28: 1000000 INFO @ Sun, 21 Jun 2020 19:34:34: 2000000 INFO @ Sun, 21 Jun 2020 19:34:40: 3000000 INFO @ Sun, 21 Jun 2020 19:34:46: 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 19:34:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287830/SRX287830.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287830/SRX287830.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287830/SRX287830.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287830/SRX287830.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 19:34:51: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:34:51: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:34:53: 5000000 INFO @ Sun, 21 Jun 2020 19:34:58: 1000000 INFO @ Sun, 21 Jun 2020 19:34:59: 6000000 INFO @ Sun, 21 Jun 2020 19:35:05: 2000000 INFO @ Sun, 21 Jun 2020 19:35:06: 7000000 INFO @ Sun, 21 Jun 2020 19:35:11: 3000000 INFO @ Sun, 21 Jun 2020 19:35:12: 8000000 INFO @ Sun, 21 Jun 2020 19:35:18: 4000000 INFO @ Sun, 21 Jun 2020 19:35:19: 9000000 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 19:35:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287830/SRX287830.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287830/SRX287830.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287830/SRX287830.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287830/SRX287830.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 19:35:21: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:35:21: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:35:24: 5000000 INFO @ Sun, 21 Jun 2020 19:35:26: 10000000 INFO @ Sun, 21 Jun 2020 19:35:28: 1000000 INFO @ Sun, 21 Jun 2020 19:35:31: 6000000 INFO @ Sun, 21 Jun 2020 19:35:33: 11000000 INFO @ Sun, 21 Jun 2020 19:35:35: 2000000 INFO @ Sun, 21 Jun 2020 19:35:38: 7000000 INFO @ Sun, 21 Jun 2020 19:35:40: 12000000 INFO @ Sun, 21 Jun 2020 19:35:42: 3000000 INFO @ Sun, 21 Jun 2020 19:35:44: 8000000 INFO @ Sun, 21 Jun 2020 19:35:47: 13000000 INFO @ Sun, 21 Jun 2020 19:35:49: 4000000 INFO @ Sun, 21 Jun 2020 19:35:50: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:35:50: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:35:50: #1 total tags in treatment: 13434482 INFO @ Sun, 21 Jun 2020 19:35:50: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:35:50: #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 19:35:50: #1 tags after filtering in treatment: 13434482 INFO @ Sun, 21 Jun 2020 19:35:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:35:50: #1 finished! INFO @ Sun, 21 Jun 2020 19:35:50: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:35:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:35:51: 9000000 INFO @ Sun, 21 Jun 2020 19:35:51: #2 number of paired peaks: 431 WARNING @ Sun, 21 Jun 2020 19:35:51: Fewer paired peaks (431) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 431 pairs to build model! INFO @ Sun, 21 Jun 2020 19:35:51: start model_add_line... INFO @ Sun, 21 Jun 2020 19:35:51: start X-correlation... INFO @ Sun, 21 Jun 2020 19:35:51: end of X-cor INFO @ Sun, 21 Jun 2020 19:35:51: #2 finished! INFO @ Sun, 21 Jun 2020 19:35:51: #2 predicted fragment length is 43 bps INFO @ Sun, 21 Jun 2020 19:35:51: #2 alternative fragment length(s) may be 3,43 bps INFO @ Sun, 21 Jun 2020 19:35:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287830/SRX287830.05_model.r WARNING @ Sun, 21 Jun 2020 19:35:51: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:35:51: #2 You may need to consider one of the other alternative d(s): 3,43 WARNING @ Sun, 21 Jun 2020 19:35:51: #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 19:35:51: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:35:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:35:55: 5000000 INFO @ Sun, 21 Jun 2020 19:35:58: 10000000 INFO @ Sun, 21 Jun 2020 19:36:01: 6000000 INFO @ Sun, 21 Jun 2020 19:36:04: 11000000 INFO @ Sun, 21 Jun 2020 19:36:08: 7000000 INFO @ Sun, 21 Jun 2020 19:36:11: 12000000 INFO @ Sun, 21 Jun 2020 19:36:15: 8000000 INFO @ Sun, 21 Jun 2020 19:36:16: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:36:18: 13000000 INFO @ Sun, 21 Jun 2020 19:36:21: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:36:21: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:36:21: #1 total tags in treatment: 13434482 INFO @ Sun, 21 Jun 2020 19:36:21: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:36:21: #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 19:36:21: 9000000 INFO @ Sun, 21 Jun 2020 19:36:21: #1 tags after filtering in treatment: 13434482 INFO @ Sun, 21 Jun 2020 19:36:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:36:21: #1 finished! INFO @ Sun, 21 Jun 2020 19:36:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:36:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:36:22: #2 number of paired peaks: 431 WARNING @ Sun, 21 Jun 2020 19:36:22: Fewer paired peaks (431) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 431 pairs to build model! INFO @ Sun, 21 Jun 2020 19:36:22: start model_add_line... INFO @ Sun, 21 Jun 2020 19:36:22: start X-correlation... INFO @ Sun, 21 Jun 2020 19:36:22: end of X-cor INFO @ Sun, 21 Jun 2020 19:36:22: #2 finished! INFO @ Sun, 21 Jun 2020 19:36:22: #2 predicted fragment length is 43 bps INFO @ Sun, 21 Jun 2020 19:36:22: #2 alternative fragment length(s) may be 3,43 bps INFO @ Sun, 21 Jun 2020 19:36:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287830/SRX287830.10_model.r WARNING @ Sun, 21 Jun 2020 19:36:22: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:36:22: #2 You may need to consider one of the other alternative d(s): 3,43 WARNING @ Sun, 21 Jun 2020 19:36:22: #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 19:36:22: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:36:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:36:28: 10000000 INFO @ Sun, 21 Jun 2020 19:36:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287830/SRX287830.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:36:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287830/SRX287830.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:36:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287830/SRX287830.05_summits.bed INFO @ Sun, 21 Jun 2020 19:36:28: Done! pass1 - making usageList (610 chroms): 1 millis pass2 - checking and writing primary data (2453 records, 4 fields): 18 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:36:34: 11000000 INFO @ Sun, 21 Jun 2020 19:36:40: 12000000 INFO @ Sun, 21 Jun 2020 19:36:46: 13000000 INFO @ Sun, 21 Jun 2020 19:36:48: #3 Call peaks for each chromosome... 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: 13434482 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 19:36:50: #1 tags after filtering in treatment: 13434482 INFO @ Sun, 21 Jun 2020 19:36:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:36:50: #1 finished! INFO @ Sun, 21 Jun 2020 19:36:50: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:36:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:36:51: #2 number of paired peaks: 431 WARNING @ Sun, 21 Jun 2020 19:36:51: Fewer paired peaks (431) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 431 pairs to build model! INFO @ Sun, 21 Jun 2020 19:36:51: start model_add_line... INFO @ Sun, 21 Jun 2020 19:36:51: start X-correlation... INFO @ Sun, 21 Jun 2020 19:36:51: end of X-cor INFO @ Sun, 21 Jun 2020 19:36:51: #2 finished! INFO @ Sun, 21 Jun 2020 19:36:51: #2 predicted fragment length is 43 bps INFO @ Sun, 21 Jun 2020 19:36:51: #2 alternative fragment length(s) may be 3,43 bps INFO @ Sun, 21 Jun 2020 19:36:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287830/SRX287830.20_model.r WARNING @ Sun, 21 Jun 2020 19:36:51: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:36:51: #2 You may need to consider one of the other alternative d(s): 3,43 WARNING @ Sun, 21 Jun 2020 19:36:51: #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 19:36:51: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:36:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:37:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287830/SRX287830.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:37:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287830/SRX287830.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:37:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287830/SRX287830.10_summits.bed INFO @ Sun, 21 Jun 2020 19:37:01: Done! pass1 - making usageList (502 chroms): 1 millis pass2 - checking and writing primary data (1721 records, 4 fields): 14 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:37:15: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:37:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287830/SRX287830.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:37:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287830/SRX287830.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:37:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287830/SRX287830.20_summits.bed INFO @ Sun, 21 Jun 2020 19:37:28: Done! pass1 - making usageList (272 chroms): 1 millis pass2 - checking and writing primary data (569 records, 4 fields): 9 millis CompletedMACS2peakCalling