Job ID = 6456290 SRX = SRX335495 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:49:46 prefetch.2.10.7: 1) Downloading 'SRR952837'... 2020-06-21T10:49:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:52:16 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:52:16 prefetch.2.10.7: 1) 'SRR952837' was downloaded successfully Read 25341638 spots for SRR952837/SRR952837.sra Written 25341638 spots for SRR952837/SRR952837.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: 00:08:31 25341638 reads; of these: 25341638 (100.00%) were unpaired; of these: 8991284 (35.48%) aligned 0 times 8908343 (35.15%) aligned exactly 1 time 7442011 (29.37%) aligned >1 times 64.52% overall alignment rate Time searching: 00:08:31 Overall time: 00:08:31 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] 8056065 / 16350354 = 0.4927 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 20:06:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX335495/SRX335495.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX335495/SRX335495.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX335495/SRX335495.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX335495/SRX335495.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 20:06:46: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:06:46: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:06:52: 1000000 INFO @ Sun, 21 Jun 2020 20:06:57: 2000000 INFO @ Sun, 21 Jun 2020 20:07:03: 3000000 INFO @ Sun, 21 Jun 2020 20:07:09: 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 20:07:14: 5000000 INFO @ Sun, 21 Jun 2020 20:07:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX335495/SRX335495.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX335495/SRX335495.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX335495/SRX335495.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX335495/SRX335495.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 20:07:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:07:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:07:20: 6000000 INFO @ Sun, 21 Jun 2020 20:07:22: 1000000 INFO @ Sun, 21 Jun 2020 20:07:27: 7000000 INFO @ Sun, 21 Jun 2020 20:07:29: 2000000 INFO @ Sun, 21 Jun 2020 20:07:34: 8000000 INFO @ Sun, 21 Jun 2020 20:07:35: 3000000 INFO @ Sun, 21 Jun 2020 20:07:36: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:07:36: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:07:36: #1 total tags in treatment: 8294289 INFO @ Sun, 21 Jun 2020 20:07:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:07:36: #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 20:07:36: #1 tags after filtering in treatment: 8294207 INFO @ Sun, 21 Jun 2020 20:07:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:07:36: #1 finished! INFO @ Sun, 21 Jun 2020 20:07:36: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:07:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:07:37: #2 number of paired peaks: 2288 INFO @ Sun, 21 Jun 2020 20:07:37: start model_add_line... INFO @ Sun, 21 Jun 2020 20:07:37: start X-correlation... INFO @ Sun, 21 Jun 2020 20:07:37: end of X-cor INFO @ Sun, 21 Jun 2020 20:07:37: #2 finished! INFO @ Sun, 21 Jun 2020 20:07:37: #2 predicted fragment length is 52 bps INFO @ Sun, 21 Jun 2020 20:07:37: #2 alternative fragment length(s) may be 3,52,90,135,182,222,309,406,447,494,541,586 bps INFO @ Sun, 21 Jun 2020 20:07:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX335495/SRX335495.05_model.r WARNING @ Sun, 21 Jun 2020 20:07:37: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:07:37: #2 You may need to consider one of the other alternative d(s): 3,52,90,135,182,222,309,406,447,494,541,586 WARNING @ Sun, 21 Jun 2020 20:07:37: #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 20:07:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:07:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:07:41: 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 20:07:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX335495/SRX335495.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX335495/SRX335495.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX335495/SRX335495.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX335495/SRX335495.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 20:07:46: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:07:46: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:07:46: 5000000 INFO @ Sun, 21 Jun 2020 20:07:51: 1000000 INFO @ Sun, 21 Jun 2020 20:07:52: 6000000 INFO @ Sun, 21 Jun 2020 20:07:54: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:07:57: 2000000 INFO @ Sun, 21 Jun 2020 20:07:59: 7000000 INFO @ Sun, 21 Jun 2020 20:08:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX335495/SRX335495.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:08:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX335495/SRX335495.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:08:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX335495/SRX335495.05_summits.bed INFO @ Sun, 21 Jun 2020 20:08:02: Done! INFO @ Sun, 21 Jun 2020 20:08:03: 3000000 pass1 - making usageList (715 chroms): 2 millis pass2 - checking and writing primary data (2696 records, 4 fields): 44 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:08:05: 8000000 INFO @ Sun, 21 Jun 2020 20:08:07: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:08:07: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:08:07: #1 total tags in treatment: 8294289 INFO @ Sun, 21 Jun 2020 20:08:07: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:08:07: #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 20:08:07: #1 tags after filtering in treatment: 8294207 INFO @ Sun, 21 Jun 2020 20:08:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:08:07: #1 finished! INFO @ Sun, 21 Jun 2020 20:08:07: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:08:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:08:08: #2 number of paired peaks: 2288 INFO @ Sun, 21 Jun 2020 20:08:08: start model_add_line... INFO @ Sun, 21 Jun 2020 20:08:08: 4000000 INFO @ Sun, 21 Jun 2020 20:08:08: start X-correlation... INFO @ Sun, 21 Jun 2020 20:08:08: end of X-cor INFO @ Sun, 21 Jun 2020 20:08:08: #2 finished! INFO @ Sun, 21 Jun 2020 20:08:08: #2 predicted fragment length is 52 bps INFO @ Sun, 21 Jun 2020 20:08:08: #2 alternative fragment length(s) may be 3,52,90,135,182,222,309,406,447,494,541,586 bps INFO @ Sun, 21 Jun 2020 20:08:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX335495/SRX335495.10_model.r WARNING @ Sun, 21 Jun 2020 20:08:08: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:08:08: #2 You may need to consider one of the other alternative d(s): 3,52,90,135,182,222,309,406,447,494,541,586 WARNING @ Sun, 21 Jun 2020 20:08:08: #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 20:08:08: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:08:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:08:13: 5000000 INFO @ Sun, 21 Jun 2020 20:08:19: 6000000 INFO @ Sun, 21 Jun 2020 20:08:25: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:08:25: 7000000 INFO @ Sun, 21 Jun 2020 20:08:30: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:08:32: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:08:32: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:08:32: #1 total tags in treatment: 8294289 INFO @ Sun, 21 Jun 2020 20:08:32: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:08:32: #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 20:08:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX335495/SRX335495.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:08:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX335495/SRX335495.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:08:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX335495/SRX335495.10_summits.bed INFO @ Sun, 21 Jun 2020 20:08:33: Done! INFO @ Sun, 21 Jun 2020 20:08:33: #1 tags after filtering in treatment: 8294207 INFO @ Sun, 21 Jun 2020 20:08:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:08:33: #1 finished! INFO @ Sun, 21 Jun 2020 20:08:33: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:08:33: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (574 chroms): 1 millis pass2 - checking and writing primary data (1962 records, 4 fields): 33 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:08:34: #2 number of paired peaks: 2288 INFO @ Sun, 21 Jun 2020 20:08:34: start model_add_line... INFO @ Sun, 21 Jun 2020 20:08:34: start X-correlation... INFO @ Sun, 21 Jun 2020 20:08:34: end of X-cor INFO @ Sun, 21 Jun 2020 20:08:34: #2 finished! INFO @ Sun, 21 Jun 2020 20:08:34: #2 predicted fragment length is 52 bps INFO @ Sun, 21 Jun 2020 20:08:34: #2 alternative fragment length(s) may be 3,52,90,135,182,222,309,406,447,494,541,586 bps INFO @ Sun, 21 Jun 2020 20:08:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX335495/SRX335495.20_model.r WARNING @ Sun, 21 Jun 2020 20:08:34: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:08:34: #2 You may need to consider one of the other alternative d(s): 3,52,90,135,182,222,309,406,447,494,541,586 WARNING @ Sun, 21 Jun 2020 20:08:34: #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 20:08:34: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:08:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:08:51: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:08:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX335495/SRX335495.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:08:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX335495/SRX335495.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:08:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX335495/SRX335495.20_summits.bed INFO @ Sun, 21 Jun 2020 20:08:59: Done! pass1 - making usageList (392 chroms): 1 millis pass2 - checking and writing primary data (1091 records, 4 fields): 23 millis CompletedMACS2peakCalling