Job ID = 6454270 SRX = SRX193628 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:15:54 prefetch.2.10.7: 1) Downloading 'SRR586006'... 2020-06-21T09:15:54 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:18:51 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:18:52 prefetch.2.10.7: 'SRR586006' is valid 2020-06-21T09:18:52 prefetch.2.10.7: 1) 'SRR586006' was downloaded successfully Read 12186260 spots for SRR586006/SRR586006.sra Written 12186260 spots for SRR586006/SRR586006.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: 00:02:46 12186260 reads; of these: 12186260 (100.00%) were unpaired; of these: 2311683 (18.97%) aligned 0 times 7543611 (61.90%) aligned exactly 1 time 2330966 (19.13%) aligned >1 times 81.03% overall alignment rate Time searching: 00:02:46 Overall time: 00:02:46 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] 1642001 / 9874577 = 0.1663 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 18:25:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX193628/SRX193628.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX193628/SRX193628.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX193628/SRX193628.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX193628/SRX193628.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 18:25:18: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:25:18: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:25:24: 1000000 INFO @ Sun, 21 Jun 2020 18:25:30: 2000000 INFO @ Sun, 21 Jun 2020 18:25:36: 3000000 INFO @ Sun, 21 Jun 2020 18:25:42: 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 18:25:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX193628/SRX193628.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX193628/SRX193628.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX193628/SRX193628.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX193628/SRX193628.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 18:25:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:25:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:25:49: 5000000 INFO @ Sun, 21 Jun 2020 18:25:55: 1000000 INFO @ Sun, 21 Jun 2020 18:25:56: 6000000 INFO @ Sun, 21 Jun 2020 18:26:04: 7000000 INFO @ Sun, 21 Jun 2020 18:26:04: 2000000 INFO @ Sun, 21 Jun 2020 18:26:11: 8000000 INFO @ Sun, 21 Jun 2020 18:26:13: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:26:13: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:26:13: #1 total tags in treatment: 8232576 INFO @ Sun, 21 Jun 2020 18:26:13: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:26:13: #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 18:26:13: 3000000 INFO @ Sun, 21 Jun 2020 18:26:13: #1 tags after filtering in treatment: 8232470 INFO @ Sun, 21 Jun 2020 18:26:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:26:13: #1 finished! INFO @ Sun, 21 Jun 2020 18:26:13: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:26:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:26:14: #2 number of paired peaks: 565 WARNING @ Sun, 21 Jun 2020 18:26:14: Fewer paired peaks (565) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 565 pairs to build model! INFO @ Sun, 21 Jun 2020 18:26:14: start model_add_line... INFO @ Sun, 21 Jun 2020 18:26:14: start X-correlation... INFO @ Sun, 21 Jun 2020 18:26:14: end of X-cor INFO @ Sun, 21 Jun 2020 18:26:14: #2 finished! INFO @ Sun, 21 Jun 2020 18:26:14: #2 predicted fragment length is 86 bps INFO @ Sun, 21 Jun 2020 18:26:14: #2 alternative fragment length(s) may be 4,86,138,155 bps INFO @ Sun, 21 Jun 2020 18:26:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX193628/SRX193628.05_model.r WARNING @ Sun, 21 Jun 2020 18:26:14: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:26:14: #2 You may need to consider one of the other alternative d(s): 4,86,138,155 WARNING @ Sun, 21 Jun 2020 18:26:14: #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 18:26:14: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:26:14: #3 Pre-compute pvalue-qvalue table... 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 18:26:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX193628/SRX193628.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX193628/SRX193628.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX193628/SRX193628.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX193628/SRX193628.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 18:26:17: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:26:17: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:26:20: 4000000 INFO @ Sun, 21 Jun 2020 18:26:24: 1000000 INFO @ Sun, 21 Jun 2020 18:26:28: 5000000 INFO @ Sun, 21 Jun 2020 18:26:32: 2000000 INFO @ Sun, 21 Jun 2020 18:26:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:26:36: 6000000 INFO @ Sun, 21 Jun 2020 18:26:39: 3000000 INFO @ Sun, 21 Jun 2020 18:26:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX193628/SRX193628.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:26:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX193628/SRX193628.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:26:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX193628/SRX193628.05_summits.bed INFO @ Sun, 21 Jun 2020 18:26:42: Done! pass1 - making usageList (532 chroms): 2 millis pass2 - checking and writing primary data (2148 records, 4 fields): 32 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:26:45: 7000000 INFO @ Sun, 21 Jun 2020 18:26:47: 4000000 INFO @ Sun, 21 Jun 2020 18:26:52: 8000000 INFO @ Sun, 21 Jun 2020 18:26:54: 5000000 INFO @ Sun, 21 Jun 2020 18:26:54: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:26:54: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:26:54: #1 total tags in treatment: 8232576 INFO @ Sun, 21 Jun 2020 18:26:54: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:26:54: #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 18:26:55: #1 tags after filtering in treatment: 8232470 INFO @ Sun, 21 Jun 2020 18:26:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:26:55: #1 finished! INFO @ Sun, 21 Jun 2020 18:26:55: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:26:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:26:55: #2 number of paired peaks: 565 WARNING @ Sun, 21 Jun 2020 18:26:55: Fewer paired peaks (565) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 565 pairs to build model! INFO @ Sun, 21 Jun 2020 18:26:55: start model_add_line... INFO @ Sun, 21 Jun 2020 18:26:55: start X-correlation... INFO @ Sun, 21 Jun 2020 18:26:55: end of X-cor INFO @ Sun, 21 Jun 2020 18:26:55: #2 finished! INFO @ Sun, 21 Jun 2020 18:26:55: #2 predicted fragment length is 86 bps INFO @ Sun, 21 Jun 2020 18:26:55: #2 alternative fragment length(s) may be 4,86,138,155 bps INFO @ Sun, 21 Jun 2020 18:26:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX193628/SRX193628.10_model.r WARNING @ Sun, 21 Jun 2020 18:26:55: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:26:55: #2 You may need to consider one of the other alternative d(s): 4,86,138,155 WARNING @ Sun, 21 Jun 2020 18:26:55: #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 18:26:55: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:26:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:27:01: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:27:07: 7000000 INFO @ Sun, 21 Jun 2020 18:27:12: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:27:13: 8000000 INFO @ Sun, 21 Jun 2020 18:27:15: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:27:15: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:27:15: #1 total tags in treatment: 8232576 INFO @ Sun, 21 Jun 2020 18:27:15: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:27:15: #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 18:27:15: #1 tags after filtering in treatment: 8232470 INFO @ Sun, 21 Jun 2020 18:27:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:27:15: #1 finished! INFO @ Sun, 21 Jun 2020 18:27:15: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:27:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:27:16: #2 number of paired peaks: 565 WARNING @ Sun, 21 Jun 2020 18:27:16: Fewer paired peaks (565) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 565 pairs to build model! INFO @ Sun, 21 Jun 2020 18:27:16: start model_add_line... INFO @ Sun, 21 Jun 2020 18:27:16: start X-correlation... INFO @ Sun, 21 Jun 2020 18:27:16: end of X-cor INFO @ Sun, 21 Jun 2020 18:27:16: #2 finished! INFO @ Sun, 21 Jun 2020 18:27:16: #2 predicted fragment length is 86 bps INFO @ Sun, 21 Jun 2020 18:27:16: #2 alternative fragment length(s) may be 4,86,138,155 bps INFO @ Sun, 21 Jun 2020 18:27:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX193628/SRX193628.20_model.r WARNING @ Sun, 21 Jun 2020 18:27:16: #2 Since the d (86) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:27:16: #2 You may need to consider one of the other alternative d(s): 4,86,138,155 WARNING @ Sun, 21 Jun 2020 18:27:16: #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 18:27:16: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:27:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:27:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX193628/SRX193628.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:27:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX193628/SRX193628.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:27:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX193628/SRX193628.10_summits.bed INFO @ Sun, 21 Jun 2020 18:27:21: Done! pass1 - making usageList (400 chroms): 2 millis pass2 - checking and writing primary data (1034 records, 4 fields): 15 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:27:35: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:27:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX193628/SRX193628.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:27:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX193628/SRX193628.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:27:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX193628/SRX193628.20_summits.bed INFO @ Sun, 21 Jun 2020 18:27:45: Done! pass1 - making usageList (188 chroms): 1 millis pass2 - checking and writing primary data (365 records, 4 fields): 8 millis CompletedMACS2peakCalling