Job ID = 6459861 SRX = SRX914957 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:45:19 prefetch.2.10.7: 1) Downloading 'SRR1873267'... 2020-06-21T13:45:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:47:25 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:47:26 prefetch.2.10.7: 'SRR1873267' is valid 2020-06-21T13:47:26 prefetch.2.10.7: 1) 'SRR1873267' was downloaded successfully Read 19174550 spots for SRR1873267/SRR1873267.sra Written 19174550 spots for SRR1873267/SRR1873267.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: 00:03:46 19174550 reads; of these: 19174550 (100.00%) were unpaired; of these: 2691375 (14.04%) aligned 0 times 14660853 (76.46%) aligned exactly 1 time 1822322 (9.50%) aligned >1 times 85.96% overall alignment rate Time searching: 00:03:46 Overall time: 00:03:46 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] 5063358 / 16483175 = 0.3072 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 22:55:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX914957/SRX914957.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX914957/SRX914957.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX914957/SRX914957.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX914957/SRX914957.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 22:55:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:55:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:56:03: 1000000 INFO @ Sun, 21 Jun 2020 22:56:08: 2000000 INFO @ Sun, 21 Jun 2020 22:56:14: 3000000 INFO @ Sun, 21 Jun 2020 22:56:20: 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 22:56:25: 5000000 INFO @ Sun, 21 Jun 2020 22:56:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX914957/SRX914957.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX914957/SRX914957.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX914957/SRX914957.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX914957/SRX914957.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 22:56:27: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:56:27: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:56:32: 6000000 INFO @ Sun, 21 Jun 2020 22:56:35: 1000000 INFO @ Sun, 21 Jun 2020 22:56:39: 7000000 INFO @ Sun, 21 Jun 2020 22:56:42: 2000000 INFO @ Sun, 21 Jun 2020 22:56:47: 8000000 INFO @ Sun, 21 Jun 2020 22:56:50: 3000000 INFO @ Sun, 21 Jun 2020 22:56:54: 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 22:56:57: 4000000 INFO @ Sun, 21 Jun 2020 22:56:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX914957/SRX914957.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX914957/SRX914957.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX914957/SRX914957.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX914957/SRX914957.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 22:56:57: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:56:57: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:57:02: 10000000 INFO @ Sun, 21 Jun 2020 22:57:05: 5000000 INFO @ Sun, 21 Jun 2020 22:57:05: 1000000 INFO @ Sun, 21 Jun 2020 22:57:10: 11000000 INFO @ Sun, 21 Jun 2020 22:57:13: 6000000 INFO @ Sun, 21 Jun 2020 22:57:13: 2000000 INFO @ Sun, 21 Jun 2020 22:57:13: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 22:57:13: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 22:57:13: #1 total tags in treatment: 11419817 INFO @ Sun, 21 Jun 2020 22:57:13: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:57:13: #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 22:57:14: #1 tags after filtering in treatment: 11419671 INFO @ Sun, 21 Jun 2020 22:57:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:57:14: #1 finished! INFO @ Sun, 21 Jun 2020 22:57:14: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:57:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:57:14: #2 number of paired peaks: 270 WARNING @ Sun, 21 Jun 2020 22:57:14: Fewer paired peaks (270) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 270 pairs to build model! INFO @ Sun, 21 Jun 2020 22:57:14: start model_add_line... INFO @ Sun, 21 Jun 2020 22:57:14: start X-correlation... INFO @ Sun, 21 Jun 2020 22:57:14: end of X-cor INFO @ Sun, 21 Jun 2020 22:57:14: #2 finished! INFO @ Sun, 21 Jun 2020 22:57:14: #2 predicted fragment length is 44 bps INFO @ Sun, 21 Jun 2020 22:57:14: #2 alternative fragment length(s) may be 2,44,97,136,150,171,498,568,570,574 bps INFO @ Sun, 21 Jun 2020 22:57:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX914957/SRX914957.05_model.r WARNING @ Sun, 21 Jun 2020 22:57:14: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:57:14: #2 You may need to consider one of the other alternative d(s): 2,44,97,136,150,171,498,568,570,574 WARNING @ Sun, 21 Jun 2020 22:57:14: #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 22:57:14: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:57:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:57:20: 3000000 INFO @ Sun, 21 Jun 2020 22:57:21: 7000000 INFO @ Sun, 21 Jun 2020 22:57:28: 4000000 INFO @ Sun, 21 Jun 2020 22:57:28: 8000000 INFO @ Sun, 21 Jun 2020 22:57:35: 5000000 INFO @ Sun, 21 Jun 2020 22:57:36: 9000000 INFO @ Sun, 21 Jun 2020 22:57:38: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:57:43: 6000000 INFO @ Sun, 21 Jun 2020 22:57:44: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:57:50: 7000000 INFO @ Sun, 21 Jun 2020 22:57:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX914957/SRX914957.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:57:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX914957/SRX914957.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:57:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX914957/SRX914957.05_summits.bed INFO @ Sun, 21 Jun 2020 22:57:51: Done! pass1 - making usageList (101 chroms): 1 millis pass2 - checking and writing primary data (450 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:57:52: 11000000 INFO @ Sun, 21 Jun 2020 22:57:55: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 22:57:55: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 22:57:55: #1 total tags in treatment: 11419817 INFO @ Sun, 21 Jun 2020 22:57:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:57:55: #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 22:57:55: #1 tags after filtering in treatment: 11419671 INFO @ Sun, 21 Jun 2020 22:57:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:57:55: #1 finished! INFO @ Sun, 21 Jun 2020 22:57:55: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:57:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:57:56: #2 number of paired peaks: 270 WARNING @ Sun, 21 Jun 2020 22:57:56: Fewer paired peaks (270) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 270 pairs to build model! INFO @ Sun, 21 Jun 2020 22:57:56: start model_add_line... INFO @ Sun, 21 Jun 2020 22:57:56: start X-correlation... INFO @ Sun, 21 Jun 2020 22:57:56: end of X-cor INFO @ Sun, 21 Jun 2020 22:57:56: #2 finished! INFO @ Sun, 21 Jun 2020 22:57:56: #2 predicted fragment length is 44 bps INFO @ Sun, 21 Jun 2020 22:57:56: #2 alternative fragment length(s) may be 2,44,97,136,150,171,498,568,570,574 bps INFO @ Sun, 21 Jun 2020 22:57:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX914957/SRX914957.10_model.r WARNING @ Sun, 21 Jun 2020 22:57:56: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:57:56: #2 You may need to consider one of the other alternative d(s): 2,44,97,136,150,171,498,568,570,574 WARNING @ Sun, 21 Jun 2020 22:57:56: #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 22:57:56: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:57:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:57:58: 8000000 INFO @ Sun, 21 Jun 2020 22:58:05: 9000000 INFO @ Sun, 21 Jun 2020 22:58:12: 10000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:58:19: 11000000 INFO @ Sun, 21 Jun 2020 22:58:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:58:22: #1 tag size is determined as 40 bps INFO @ Sun, 21 Jun 2020 22:58:22: #1 tag size = 40 INFO @ Sun, 21 Jun 2020 22:58:22: #1 total tags in treatment: 11419817 INFO @ Sun, 21 Jun 2020 22:58:22: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:58:22: #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 22:58:22: #1 tags after filtering in treatment: 11419671 INFO @ Sun, 21 Jun 2020 22:58:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:58:22: #1 finished! INFO @ Sun, 21 Jun 2020 22:58:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:58:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:58:23: #2 number of paired peaks: 270 WARNING @ Sun, 21 Jun 2020 22:58:23: Fewer paired peaks (270) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 270 pairs to build model! INFO @ Sun, 21 Jun 2020 22:58:23: start model_add_line... INFO @ Sun, 21 Jun 2020 22:58:23: start X-correlation... INFO @ Sun, 21 Jun 2020 22:58:23: end of X-cor INFO @ Sun, 21 Jun 2020 22:58:23: #2 finished! INFO @ Sun, 21 Jun 2020 22:58:23: #2 predicted fragment length is 44 bps INFO @ Sun, 21 Jun 2020 22:58:23: #2 alternative fragment length(s) may be 2,44,97,136,150,171,498,568,570,574 bps INFO @ Sun, 21 Jun 2020 22:58:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX914957/SRX914957.20_model.r WARNING @ Sun, 21 Jun 2020 22:58:23: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:58:23: #2 You may need to consider one of the other alternative d(s): 2,44,97,136,150,171,498,568,570,574 WARNING @ Sun, 21 Jun 2020 22:58:23: #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 22:58:23: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:58:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:58:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX914957/SRX914957.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:58:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX914957/SRX914957.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:58:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX914957/SRX914957.10_summits.bed INFO @ Sun, 21 Jun 2020 22:58:31: Done! pass1 - making usageList (73 chroms): 0 millis pass2 - checking and writing primary data (228 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:58:46: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:58:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX914957/SRX914957.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:58:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX914957/SRX914957.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:58:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX914957/SRX914957.20_summits.bed INFO @ Sun, 21 Jun 2020 22:58:57: Done! pass1 - making usageList (45 chroms): 1 millis pass2 - checking and writing primary data (78 records, 4 fields): 2 millis CompletedMACS2peakCalling