Job ID = 6458921 SRX = SRX5775926 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:53:52 prefetch.2.10.7: 1) Downloading 'SRR8997129'... 2020-06-21T12:53:52 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:56:54 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:56:54 prefetch.2.10.7: 1) 'SRR8997129' was downloaded successfully Read 17109992 spots for SRR8997129/SRR8997129.sra Written 17109992 spots for SRR8997129/SRR8997129.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: 00:06:17 17109992 reads; of these: 17109992 (100.00%) were unpaired; of these: 711597 (4.16%) aligned 0 times 11857266 (69.30%) aligned exactly 1 time 4541129 (26.54%) aligned >1 times 95.84% overall alignment rate Time searching: 00:06:17 Overall time: 00:06:17 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] 5510892 / 16398395 = 0.3361 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 22:09:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5775926/SRX5775926.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5775926/SRX5775926.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5775926/SRX5775926.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5775926/SRX5775926.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 22:09:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:09:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:09:38: 1000000 INFO @ Sun, 21 Jun 2020 22:09:43: 2000000 INFO @ Sun, 21 Jun 2020 22:09:49: 3000000 INFO @ Sun, 21 Jun 2020 22:09:54: 4000000 INFO @ Sun, 21 Jun 2020 22:09:59: 5000000 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 22:10:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5775926/SRX5775926.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5775926/SRX5775926.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5775926/SRX5775926.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5775926/SRX5775926.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 22:10:03: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:10:03: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:10:04: 6000000 INFO @ Sun, 21 Jun 2020 22:10:08: 1000000 INFO @ Sun, 21 Jun 2020 22:10:10: 7000000 INFO @ Sun, 21 Jun 2020 22:10:14: 2000000 INFO @ Sun, 21 Jun 2020 22:10:15: 8000000 INFO @ Sun, 21 Jun 2020 22:10:19: 3000000 INFO @ Sun, 21 Jun 2020 22:10:21: 9000000 INFO @ Sun, 21 Jun 2020 22:10:25: 4000000 INFO @ Sun, 21 Jun 2020 22:10:26: 10000000 INFO @ Sun, 21 Jun 2020 22:10:30: 5000000 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 22:10:32: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 22:10:32: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 22:10:32: #1 total tags in treatment: 10887503 INFO @ Sun, 21 Jun 2020 22:10:32: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:10:32: #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 22:10:32: #1 tags after filtering in treatment: 10887500 INFO @ Sun, 21 Jun 2020 22:10:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:10:32: #1 finished! INFO @ Sun, 21 Jun 2020 22:10:32: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:10:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:10:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5775926/SRX5775926.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5775926/SRX5775926.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5775926/SRX5775926.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5775926/SRX5775926.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 22:10:33: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:10:33: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:10:33: #2 number of paired peaks: 922 WARNING @ Sun, 21 Jun 2020 22:10:33: Fewer paired peaks (922) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 922 pairs to build model! INFO @ Sun, 21 Jun 2020 22:10:33: start model_add_line... INFO @ Sun, 21 Jun 2020 22:10:33: start X-correlation... INFO @ Sun, 21 Jun 2020 22:10:33: end of X-cor INFO @ Sun, 21 Jun 2020 22:10:33: #2 finished! INFO @ Sun, 21 Jun 2020 22:10:33: #2 predicted fragment length is 71 bps INFO @ Sun, 21 Jun 2020 22:10:33: #2 alternative fragment length(s) may be 4,71 bps INFO @ Sun, 21 Jun 2020 22:10:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5775926/SRX5775926.05_model.r WARNING @ Sun, 21 Jun 2020 22:10:33: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:10:33: #2 You may need to consider one of the other alternative d(s): 4,71 WARNING @ Sun, 21 Jun 2020 22:10:33: #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 22:10:33: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:10:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:10:36: 6000000 INFO @ Sun, 21 Jun 2020 22:10:39: 1000000 INFO @ Sun, 21 Jun 2020 22:10:42: 7000000 INFO @ Sun, 21 Jun 2020 22:10:45: 2000000 INFO @ Sun, 21 Jun 2020 22:10:48: 8000000 INFO @ Sun, 21 Jun 2020 22:10:51: 3000000 INFO @ Sun, 21 Jun 2020 22:10:54: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:10:55: 9000000 INFO @ Sun, 21 Jun 2020 22:10:57: 4000000 INFO @ Sun, 21 Jun 2020 22:11:01: 10000000 INFO @ Sun, 21 Jun 2020 22:11:03: 5000000 INFO @ Sun, 21 Jun 2020 22:11:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5775926/SRX5775926.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:11:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5775926/SRX5775926.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:11:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5775926/SRX5775926.05_summits.bed INFO @ Sun, 21 Jun 2020 22:11:04: Done! pass1 - making usageList (696 chroms): 2 millis pass2 - checking and writing primary data (2158 records, 4 fields): 39 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:11:07: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 22:11:07: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 22:11:07: #1 total tags in treatment: 10887503 INFO @ Sun, 21 Jun 2020 22:11:07: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:11:07: #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 22:11:07: #1 tags after filtering in treatment: 10887500 INFO @ Sun, 21 Jun 2020 22:11:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:11:07: #1 finished! INFO @ Sun, 21 Jun 2020 22:11:07: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:11:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:11:08: #2 number of paired peaks: 922 WARNING @ Sun, 21 Jun 2020 22:11:08: Fewer paired peaks (922) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 922 pairs to build model! INFO @ Sun, 21 Jun 2020 22:11:08: start model_add_line... INFO @ Sun, 21 Jun 2020 22:11:08: start X-correlation... INFO @ Sun, 21 Jun 2020 22:11:08: end of X-cor INFO @ Sun, 21 Jun 2020 22:11:08: #2 finished! INFO @ Sun, 21 Jun 2020 22:11:08: #2 predicted fragment length is 71 bps INFO @ Sun, 21 Jun 2020 22:11:08: #2 alternative fragment length(s) may be 4,71 bps INFO @ Sun, 21 Jun 2020 22:11:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5775926/SRX5775926.10_model.r WARNING @ Sun, 21 Jun 2020 22:11:08: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:11:08: #2 You may need to consider one of the other alternative d(s): 4,71 WARNING @ Sun, 21 Jun 2020 22:11:08: #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 22:11:08: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:11:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:11:08: 6000000 INFO @ Sun, 21 Jun 2020 22:11:14: 7000000 INFO @ Sun, 21 Jun 2020 22:11:19: 8000000 INFO @ Sun, 21 Jun 2020 22:11:25: 9000000 INFO @ Sun, 21 Jun 2020 22:11:29: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:11:30: 10000000 INFO @ Sun, 21 Jun 2020 22:11:36: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 22:11:36: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 22:11:36: #1 total tags in treatment: 10887503 INFO @ Sun, 21 Jun 2020 22:11:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:11:36: #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 22:11:37: #1 tags after filtering in treatment: 10887500 INFO @ Sun, 21 Jun 2020 22:11:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:11:37: #1 finished! INFO @ Sun, 21 Jun 2020 22:11:37: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:11:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:11:38: #2 number of paired peaks: 922 WARNING @ Sun, 21 Jun 2020 22:11:38: Fewer paired peaks (922) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 922 pairs to build model! INFO @ Sun, 21 Jun 2020 22:11:38: start model_add_line... INFO @ Sun, 21 Jun 2020 22:11:38: start X-correlation... INFO @ Sun, 21 Jun 2020 22:11:38: end of X-cor INFO @ Sun, 21 Jun 2020 22:11:38: #2 finished! INFO @ Sun, 21 Jun 2020 22:11:38: #2 predicted fragment length is 71 bps INFO @ Sun, 21 Jun 2020 22:11:38: #2 alternative fragment length(s) may be 4,71 bps INFO @ Sun, 21 Jun 2020 22:11:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5775926/SRX5775926.20_model.r WARNING @ Sun, 21 Jun 2020 22:11:38: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:11:38: #2 You may need to consider one of the other alternative d(s): 4,71 WARNING @ Sun, 21 Jun 2020 22:11:38: #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 22:11:38: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:11:38: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:11:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5775926/SRX5775926.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:11:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5775926/SRX5775926.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:11:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5775926/SRX5775926.10_summits.bed INFO @ Sun, 21 Jun 2020 22:11:39: Done! pass1 - making usageList (582 chroms): 1 millis pass2 - checking and writing primary data (1624 records, 4 fields): 33 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:11:58: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:12:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5775926/SRX5775926.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:12:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5775926/SRX5775926.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:12:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5775926/SRX5775926.20_summits.bed INFO @ Sun, 21 Jun 2020 22:12:08: Done! pass1 - making usageList (436 chroms): 1 millis pass2 - checking and writing primary data (1152 records, 4 fields): 25 millis CompletedMACS2peakCalling BigWig に変換しました。