Job ID = 6458870 SRX = SRX5717040 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:41:14 prefetch.2.10.7: 1) Downloading 'SRR8936401'... 2020-06-21T12:41:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:43:41 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:43:42 prefetch.2.10.7: 'SRR8936401' is valid 2020-06-21T12:43:42 prefetch.2.10.7: 1) 'SRR8936401' was downloaded successfully Read 20427548 spots for SRR8936401/SRR8936401.sra Written 20427548 spots for SRR8936401/SRR8936401.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: 00:05:12 20427548 reads; of these: 20427548 (100.00%) were unpaired; of these: 2729777 (13.36%) aligned 0 times 12226919 (59.86%) aligned exactly 1 time 5470852 (26.78%) aligned >1 times 86.64% overall alignment rate Time searching: 00:05:12 Overall time: 00:05:12 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] 4265301 / 17697771 = 0.2410 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 21:53:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5717040/SRX5717040.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5717040/SRX5717040.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5717040/SRX5717040.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5717040/SRX5717040.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 21:53:42: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:53:42: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:53:47: 1000000 INFO @ Sun, 21 Jun 2020 21:53:52: 2000000 INFO @ Sun, 21 Jun 2020 21:53:57: 3000000 INFO @ Sun, 21 Jun 2020 21:54:02: 4000000 INFO @ Sun, 21 Jun 2020 21:54:07: 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 21:54:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5717040/SRX5717040.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5717040/SRX5717040.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5717040/SRX5717040.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5717040/SRX5717040.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 21:54:11: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:54:11: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:54:12: 6000000 INFO @ Sun, 21 Jun 2020 21:54:17: 1000000 INFO @ Sun, 21 Jun 2020 21:54:18: 7000000 INFO @ Sun, 21 Jun 2020 21:54:24: 2000000 INFO @ Sun, 21 Jun 2020 21:54:24: 8000000 INFO @ Sun, 21 Jun 2020 21:54:29: 9000000 INFO @ Sun, 21 Jun 2020 21:54:30: 3000000 INFO @ Sun, 21 Jun 2020 21:54:35: 10000000 INFO @ Sun, 21 Jun 2020 21:54:36: 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 21:54:40: 11000000 INFO @ Sun, 21 Jun 2020 21:54:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5717040/SRX5717040.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5717040/SRX5717040.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5717040/SRX5717040.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5717040/SRX5717040.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 21:54:41: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:54:41: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:54:42: 5000000 INFO @ Sun, 21 Jun 2020 21:54:47: 12000000 INFO @ Sun, 21 Jun 2020 21:54:47: 1000000 INFO @ Sun, 21 Jun 2020 21:54:49: 6000000 INFO @ Sun, 21 Jun 2020 21:54:52: 13000000 INFO @ Sun, 21 Jun 2020 21:54:54: 2000000 INFO @ Sun, 21 Jun 2020 21:54:55: 7000000 INFO @ Sun, 21 Jun 2020 21:54:55: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:54:55: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:54:55: #1 total tags in treatment: 13432470 INFO @ Sun, 21 Jun 2020 21:54:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:54:55: #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 21:54:56: #1 tags after filtering in treatment: 13432397 INFO @ Sun, 21 Jun 2020 21:54:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:54:56: #1 finished! INFO @ Sun, 21 Jun 2020 21:54:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:54:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:54:56: #2 number of paired peaks: 395 WARNING @ Sun, 21 Jun 2020 21:54:56: Fewer paired peaks (395) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 395 pairs to build model! INFO @ Sun, 21 Jun 2020 21:54:56: start model_add_line... INFO @ Sun, 21 Jun 2020 21:54:57: start X-correlation... INFO @ Sun, 21 Jun 2020 21:54:57: end of X-cor INFO @ Sun, 21 Jun 2020 21:54:57: #2 finished! INFO @ Sun, 21 Jun 2020 21:54:57: #2 predicted fragment length is 56 bps INFO @ Sun, 21 Jun 2020 21:54:57: #2 alternative fragment length(s) may be 39,56,92,149,424,450,491,530,555,593 bps INFO @ Sun, 21 Jun 2020 21:54:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5717040/SRX5717040.05_model.r WARNING @ Sun, 21 Jun 2020 21:54:57: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:54:57: #2 You may need to consider one of the other alternative d(s): 39,56,92,149,424,450,491,530,555,593 WARNING @ Sun, 21 Jun 2020 21:54:57: #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 21:54:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:54:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:55:01: 3000000 INFO @ Sun, 21 Jun 2020 21:55:01: 8000000 INFO @ Sun, 21 Jun 2020 21:55:07: 4000000 INFO @ Sun, 21 Jun 2020 21:55:08: 9000000 INFO @ Sun, 21 Jun 2020 21:55:13: 5000000 INFO @ Sun, 21 Jun 2020 21:55:14: 10000000 INFO @ Sun, 21 Jun 2020 21:55:20: 6000000 INFO @ Sun, 21 Jun 2020 21:55:20: 11000000 INFO @ Sun, 21 Jun 2020 21:55:22: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:55:26: 7000000 INFO @ Sun, 21 Jun 2020 21:55:27: 12000000 INFO @ Sun, 21 Jun 2020 21:55:32: 8000000 INFO @ Sun, 21 Jun 2020 21:55:33: 13000000 INFO @ Sun, 21 Jun 2020 21:55:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5717040/SRX5717040.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:55:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5717040/SRX5717040.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:55:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5717040/SRX5717040.05_summits.bed INFO @ Sun, 21 Jun 2020 21:55:34: Done! pass1 - making usageList (469 chroms): 1 millis pass2 - checking and writing primary data (1883 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:55:36: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:55:36: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:55:36: #1 total tags in treatment: 13432470 INFO @ Sun, 21 Jun 2020 21:55:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:55:36: #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 21:55:36: #1 tags after filtering in treatment: 13432397 INFO @ Sun, 21 Jun 2020 21:55:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:55:36: #1 finished! INFO @ Sun, 21 Jun 2020 21:55:36: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:55:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:55:37: #2 number of paired peaks: 395 WARNING @ Sun, 21 Jun 2020 21:55:37: Fewer paired peaks (395) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 395 pairs to build model! INFO @ Sun, 21 Jun 2020 21:55:37: start model_add_line... INFO @ Sun, 21 Jun 2020 21:55:37: start X-correlation... INFO @ Sun, 21 Jun 2020 21:55:37: end of X-cor INFO @ Sun, 21 Jun 2020 21:55:37: #2 finished! INFO @ Sun, 21 Jun 2020 21:55:37: #2 predicted fragment length is 56 bps INFO @ Sun, 21 Jun 2020 21:55:37: #2 alternative fragment length(s) may be 39,56,92,149,424,450,491,530,555,593 bps INFO @ Sun, 21 Jun 2020 21:55:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5717040/SRX5717040.10_model.r WARNING @ Sun, 21 Jun 2020 21:55:37: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:55:37: #2 You may need to consider one of the other alternative d(s): 39,56,92,149,424,450,491,530,555,593 WARNING @ Sun, 21 Jun 2020 21:55:37: #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 21:55:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:55:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:55:39: 9000000 INFO @ Sun, 21 Jun 2020 21:55:45: 10000000 INFO @ Sun, 21 Jun 2020 21:55:50: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:55:57: 12000000 INFO @ Sun, 21 Jun 2020 21:56:02: 13000000 INFO @ Sun, 21 Jun 2020 21:56:03: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:56:05: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:56:05: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:56:05: #1 total tags in treatment: 13432470 INFO @ Sun, 21 Jun 2020 21:56:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:56:05: #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 21:56:06: #1 tags after filtering in treatment: 13432397 INFO @ Sun, 21 Jun 2020 21:56:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:56:06: #1 finished! INFO @ Sun, 21 Jun 2020 21:56:06: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:56:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:56:07: #2 number of paired peaks: 395 WARNING @ Sun, 21 Jun 2020 21:56:07: Fewer paired peaks (395) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 395 pairs to build model! INFO @ Sun, 21 Jun 2020 21:56:07: start model_add_line... INFO @ Sun, 21 Jun 2020 21:56:07: start X-correlation... INFO @ Sun, 21 Jun 2020 21:56:07: end of X-cor INFO @ Sun, 21 Jun 2020 21:56:07: #2 finished! INFO @ Sun, 21 Jun 2020 21:56:07: #2 predicted fragment length is 56 bps INFO @ Sun, 21 Jun 2020 21:56:07: #2 alternative fragment length(s) may be 39,56,92,149,424,450,491,530,555,593 bps INFO @ Sun, 21 Jun 2020 21:56:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5717040/SRX5717040.20_model.r WARNING @ Sun, 21 Jun 2020 21:56:07: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:56:07: #2 You may need to consider one of the other alternative d(s): 39,56,92,149,424,450,491,530,555,593 WARNING @ Sun, 21 Jun 2020 21:56:07: #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 21:56:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:56:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:56:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5717040/SRX5717040.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:56:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5717040/SRX5717040.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:56:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5717040/SRX5717040.10_summits.bed INFO @ Sun, 21 Jun 2020 21:56:16: Done! pass1 - making usageList (269 chroms): 1 millis pass2 - checking and writing primary data (617 records, 4 fields): 9 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:56:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:56:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5717040/SRX5717040.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:56:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5717040/SRX5717040.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:56:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5717040/SRX5717040.20_summits.bed INFO @ Sun, 21 Jun 2020 21:56:45: Done! pass1 - making usageList (87 chroms): 1 millis pass2 - checking and writing primary data (161 records, 4 fields): 4 millis CompletedMACS2peakCalling