Job ID = 6455670 SRX = SRX287975 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:31:51 prefetch.2.10.7: 1) Downloading 'SRR870164'... 2020-06-21T10:31:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:34:22 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:34:23 prefetch.2.10.7: 'SRR870164' is valid 2020-06-21T10:34:23 prefetch.2.10.7: 1) 'SRR870164' was downloaded successfully Read 13809114 spots for SRR870164/SRR870164.sra Written 13809114 spots for SRR870164/SRR870164.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: 00:04:06 13809114 reads; of these: 13809114 (100.00%) were unpaired; of these: 756616 (5.48%) aligned 0 times 9039844 (65.46%) aligned exactly 1 time 4012654 (29.06%) aligned >1 times 94.52% overall alignment rate Time searching: 00:04:06 Overall time: 00:04:06 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] 2217090 / 13052498 = 0.1699 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 19:42:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287975/SRX287975.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287975/SRX287975.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287975/SRX287975.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287975/SRX287975.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 19:42:42: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:42:42: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:42:48: 1000000 INFO @ Sun, 21 Jun 2020 19:42:54: 2000000 INFO @ Sun, 21 Jun 2020 19:42:59: 3000000 INFO @ Sun, 21 Jun 2020 19:43:05: 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 19:43:11: 5000000 INFO @ Sun, 21 Jun 2020 19:43:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287975/SRX287975.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287975/SRX287975.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287975/SRX287975.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287975/SRX287975.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 19:43:12: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:43:12: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:43:17: 6000000 INFO @ Sun, 21 Jun 2020 19:43:18: 1000000 INFO @ Sun, 21 Jun 2020 19:43:23: 7000000 INFO @ Sun, 21 Jun 2020 19:43:24: 2000000 INFO @ Sun, 21 Jun 2020 19:43:29: 8000000 INFO @ Sun, 21 Jun 2020 19:43:31: 3000000 INFO @ Sun, 21 Jun 2020 19:43:36: 9000000 INFO @ Sun, 21 Jun 2020 19:43:37: 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 19:43:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287975/SRX287975.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287975/SRX287975.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287975/SRX287975.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287975/SRX287975.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 19:43:42: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:43:42: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:43:42: 10000000 INFO @ Sun, 21 Jun 2020 19:43:43: 5000000 INFO @ Sun, 21 Jun 2020 19:43:48: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:43:48: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:43:48: #1 total tags in treatment: 10835408 INFO @ Sun, 21 Jun 2020 19:43:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:43:48: #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 19:43:49: #1 tags after filtering in treatment: 10835408 INFO @ Sun, 21 Jun 2020 19:43:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:43:49: #1 finished! INFO @ Sun, 21 Jun 2020 19:43:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:43:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:43:49: 6000000 INFO @ Sun, 21 Jun 2020 19:43:49: #2 number of paired peaks: 694 WARNING @ Sun, 21 Jun 2020 19:43:49: Fewer paired peaks (694) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 694 pairs to build model! INFO @ Sun, 21 Jun 2020 19:43:49: start model_add_line... INFO @ Sun, 21 Jun 2020 19:43:50: start X-correlation... INFO @ Sun, 21 Jun 2020 19:43:50: end of X-cor INFO @ Sun, 21 Jun 2020 19:43:50: #2 finished! INFO @ Sun, 21 Jun 2020 19:43:50: #2 predicted fragment length is 44 bps INFO @ Sun, 21 Jun 2020 19:43:50: #2 alternative fragment length(s) may be 3,44 bps INFO @ Sun, 21 Jun 2020 19:43:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287975/SRX287975.05_model.r WARNING @ Sun, 21 Jun 2020 19:43:50: #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 19:43:50: #2 You may need to consider one of the other alternative d(s): 3,44 WARNING @ Sun, 21 Jun 2020 19:43:50: #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 19:43:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:43:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:43:50: 1000000 INFO @ Sun, 21 Jun 2020 19:43:56: 7000000 INFO @ Sun, 21 Jun 2020 19:43:58: 2000000 INFO @ Sun, 21 Jun 2020 19:44:02: 8000000 INFO @ Sun, 21 Jun 2020 19:44:06: 3000000 INFO @ Sun, 21 Jun 2020 19:44:09: 9000000 INFO @ Sun, 21 Jun 2020 19:44:12: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:44:13: 4000000 INFO @ Sun, 21 Jun 2020 19:44:16: 10000000 INFO @ Sun, 21 Jun 2020 19:44:20: 5000000 INFO @ Sun, 21 Jun 2020 19:44:21: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:44:21: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:44:21: #1 total tags in treatment: 10835408 INFO @ Sun, 21 Jun 2020 19:44:21: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:44:21: #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 19:44:22: #1 tags after filtering in treatment: 10835408 INFO @ Sun, 21 Jun 2020 19:44:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:44:22: #1 finished! INFO @ Sun, 21 Jun 2020 19:44:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:44:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:44:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287975/SRX287975.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:44:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287975/SRX287975.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:44:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287975/SRX287975.05_summits.bed INFO @ Sun, 21 Jun 2020 19:44:22: Done! INFO @ Sun, 21 Jun 2020 19:44:22: #2 number of paired peaks: 694 WARNING @ Sun, 21 Jun 2020 19:44:22: Fewer paired peaks (694) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 694 pairs to build model! INFO @ Sun, 21 Jun 2020 19:44:22: start model_add_line... INFO @ Sun, 21 Jun 2020 19:44:22: start X-correlation... INFO @ Sun, 21 Jun 2020 19:44:22: end of X-cor INFO @ Sun, 21 Jun 2020 19:44:22: #2 finished! INFO @ Sun, 21 Jun 2020 19:44:22: #2 predicted fragment length is 44 bps INFO @ Sun, 21 Jun 2020 19:44:22: #2 alternative fragment length(s) may be 3,44 bps INFO @ Sun, 21 Jun 2020 19:44:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287975/SRX287975.10_model.r WARNING @ Sun, 21 Jun 2020 19:44:22: #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 19:44:22: #2 You may need to consider one of the other alternative d(s): 3,44 WARNING @ Sun, 21 Jun 2020 19:44:22: #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 19:44:22: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:44:22: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (570 chroms): 1 millis pass2 - checking and writing primary data (2213 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:44:27: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:44:34: 7000000 INFO @ Sun, 21 Jun 2020 19:44:40: 8000000 INFO @ Sun, 21 Jun 2020 19:44:44: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:44:47: 9000000 INFO @ Sun, 21 Jun 2020 19:44:54: 10000000 INFO @ Sun, 21 Jun 2020 19:44:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287975/SRX287975.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:44:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287975/SRX287975.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:44:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287975/SRX287975.10_summits.bed INFO @ Sun, 21 Jun 2020 19:44:55: Done! pass1 - making usageList (486 chroms): 1 millis pass2 - checking and writing primary data (1794 records, 4 fields): 14 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:45:00: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:45:00: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:45:00: #1 total tags in treatment: 10835408 INFO @ Sun, 21 Jun 2020 19:45:00: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:45:00: #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 19:45:00: #1 tags after filtering in treatment: 10835408 INFO @ Sun, 21 Jun 2020 19:45:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:45:00: #1 finished! INFO @ Sun, 21 Jun 2020 19:45:00: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:45:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:45:01: #2 number of paired peaks: 694 WARNING @ Sun, 21 Jun 2020 19:45:01: Fewer paired peaks (694) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 694 pairs to build model! INFO @ Sun, 21 Jun 2020 19:45:01: start model_add_line... INFO @ Sun, 21 Jun 2020 19:45:01: start X-correlation... INFO @ Sun, 21 Jun 2020 19:45:01: end of X-cor INFO @ Sun, 21 Jun 2020 19:45:01: #2 finished! INFO @ Sun, 21 Jun 2020 19:45:01: #2 predicted fragment length is 44 bps INFO @ Sun, 21 Jun 2020 19:45:01: #2 alternative fragment length(s) may be 3,44 bps INFO @ Sun, 21 Jun 2020 19:45:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287975/SRX287975.20_model.r WARNING @ Sun, 21 Jun 2020 19:45:01: #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 19:45:01: #2 You may need to consider one of the other alternative d(s): 3,44 WARNING @ Sun, 21 Jun 2020 19:45:01: #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 19:45:01: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:45:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:45:23: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:45:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287975/SRX287975.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:45:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287975/SRX287975.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:45:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287975/SRX287975.20_summits.bed INFO @ Sun, 21 Jun 2020 19:45:33: Done! pass1 - making usageList (331 chroms): 1 millis pass2 - checking and writing primary data (695 records, 4 fields): 9 millis CompletedMACS2peakCalling