Job ID = 6455597 SRX = SRX287917 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:13:51 prefetch.2.10.7: 1) Downloading 'SRR870106'... 2020-06-21T10:13:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:17:55 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:17:55 prefetch.2.10.7: 1) 'SRR870106' was downloaded successfully Read 16164431 spots for SRR870106/SRR870106.sra Written 16164431 spots for SRR870106/SRR870106.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: 00:04:40 16164431 reads; of these: 16164431 (100.00%) were unpaired; of these: 1194535 (7.39%) aligned 0 times 11266241 (69.70%) aligned exactly 1 time 3703655 (22.91%) aligned >1 times 92.61% overall alignment rate Time searching: 00:04:40 Overall time: 00:04:40 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] 1685516 / 14969896 = 0.1126 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 19:28:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287917/SRX287917.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287917/SRX287917.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287917/SRX287917.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287917/SRX287917.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 19:28:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:28:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:28:55: 1000000 INFO @ Sun, 21 Jun 2020 19:29:03: 2000000 INFO @ Sun, 21 Jun 2020 19:29:12: 3000000 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 19:29:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287917/SRX287917.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287917/SRX287917.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287917/SRX287917.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287917/SRX287917.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 19:29:17: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:29:17: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:29:21: 4000000 INFO @ Sun, 21 Jun 2020 19:29:25: 1000000 INFO @ Sun, 21 Jun 2020 19:29:30: 5000000 INFO @ Sun, 21 Jun 2020 19:29:33: 2000000 INFO @ Sun, 21 Jun 2020 19:29:39: 6000000 INFO @ Sun, 21 Jun 2020 19:29:40: 3000000 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 19:29:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287917/SRX287917.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287917/SRX287917.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287917/SRX287917.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287917/SRX287917.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 19:29:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:29:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:29:48: 7000000 INFO @ Sun, 21 Jun 2020 19:29:48: 4000000 INFO @ Sun, 21 Jun 2020 19:29:56: 1000000 INFO @ Sun, 21 Jun 2020 19:29:56: 5000000 INFO @ Sun, 21 Jun 2020 19:29:57: 8000000 INFO @ Sun, 21 Jun 2020 19:30:03: 6000000 INFO @ Sun, 21 Jun 2020 19:30:03: 2000000 INFO @ Sun, 21 Jun 2020 19:30:06: 9000000 INFO @ Sun, 21 Jun 2020 19:30:10: 7000000 INFO @ Sun, 21 Jun 2020 19:30:10: 3000000 INFO @ Sun, 21 Jun 2020 19:30:15: 10000000 INFO @ Sun, 21 Jun 2020 19:30:17: 8000000 INFO @ Sun, 21 Jun 2020 19:30:18: 4000000 INFO @ Sun, 21 Jun 2020 19:30:24: 9000000 INFO @ Sun, 21 Jun 2020 19:30:26: 5000000 INFO @ Sun, 21 Jun 2020 19:30:26: 11000000 INFO @ Sun, 21 Jun 2020 19:30:32: 10000000 INFO @ Sun, 21 Jun 2020 19:30:33: 6000000 INFO @ Sun, 21 Jun 2020 19:30:35: 12000000 INFO @ Sun, 21 Jun 2020 19:30:39: 11000000 INFO @ Sun, 21 Jun 2020 19:30:41: 7000000 INFO @ Sun, 21 Jun 2020 19:30:44: 13000000 INFO @ Sun, 21 Jun 2020 19:30:46: 12000000 INFO @ Sun, 21 Jun 2020 19:30:46: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:30:46: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:30:46: #1 total tags in treatment: 13284380 INFO @ Sun, 21 Jun 2020 19:30:46: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:30:46: #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 19:30:47: #1 tags after filtering in treatment: 13284380 INFO @ Sun, 21 Jun 2020 19:30:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:30:47: #1 finished! INFO @ Sun, 21 Jun 2020 19:30:47: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:30:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:30:48: #2 number of paired peaks: 379 WARNING @ Sun, 21 Jun 2020 19:30:48: Fewer paired peaks (379) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 379 pairs to build model! INFO @ Sun, 21 Jun 2020 19:30:48: start model_add_line... INFO @ Sun, 21 Jun 2020 19:30:48: start X-correlation... INFO @ Sun, 21 Jun 2020 19:30:48: end of X-cor INFO @ Sun, 21 Jun 2020 19:30:48: #2 finished! INFO @ Sun, 21 Jun 2020 19:30:48: #2 predicted fragment length is 44 bps INFO @ Sun, 21 Jun 2020 19:30:48: #2 alternative fragment length(s) may be 4,44 bps INFO @ Sun, 21 Jun 2020 19:30:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287917/SRX287917.05_model.r WARNING @ Sun, 21 Jun 2020 19:30:48: #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 19:30:48: #2 You may need to consider one of the other alternative d(s): 4,44 WARNING @ Sun, 21 Jun 2020 19:30:48: #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 19:30:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:30:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:30:49: 8000000 INFO @ Sun, 21 Jun 2020 19:30:54: 13000000 INFO @ Sun, 21 Jun 2020 19:30:55: 9000000 INFO @ Sun, 21 Jun 2020 19:30:56: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:30:56: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:30:56: #1 total tags in treatment: 13284380 INFO @ Sun, 21 Jun 2020 19:30:56: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:30:56: #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 19:30:56: #1 tags after filtering in treatment: 13284380 INFO @ Sun, 21 Jun 2020 19:30:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:30:56: #1 finished! INFO @ Sun, 21 Jun 2020 19:30:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:30:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:30:57: #2 number of paired peaks: 379 WARNING @ Sun, 21 Jun 2020 19:30:57: Fewer paired peaks (379) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 379 pairs to build model! INFO @ Sun, 21 Jun 2020 19:30:57: start model_add_line... INFO @ Sun, 21 Jun 2020 19:30:57: start X-correlation... INFO @ Sun, 21 Jun 2020 19:30:57: end of X-cor INFO @ Sun, 21 Jun 2020 19:30:57: #2 finished! INFO @ Sun, 21 Jun 2020 19:30:57: #2 predicted fragment length is 44 bps INFO @ Sun, 21 Jun 2020 19:30:57: #2 alternative fragment length(s) may be 4,44 bps INFO @ Sun, 21 Jun 2020 19:30:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287917/SRX287917.10_model.r WARNING @ Sun, 21 Jun 2020 19:30:57: #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 19:30:57: #2 You may need to consider one of the other alternative d(s): 4,44 WARNING @ Sun, 21 Jun 2020 19:30:57: #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 19:30:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:30:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:31:02: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:31:09: 11000000 INFO @ Sun, 21 Jun 2020 19:31:12: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:31:15: 12000000 INFO @ Sun, 21 Jun 2020 19:31:20: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:31:22: 13000000 INFO @ Sun, 21 Jun 2020 19:31:24: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:31:24: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:31:24: #1 total tags in treatment: 13284380 INFO @ Sun, 21 Jun 2020 19:31:24: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:31:24: #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 19:31:24: #1 tags after filtering in treatment: 13284380 INFO @ Sun, 21 Jun 2020 19:31:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:31:24: #1 finished! INFO @ Sun, 21 Jun 2020 19:31:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:31:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:31:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287917/SRX287917.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:31:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287917/SRX287917.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:31:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287917/SRX287917.05_summits.bed INFO @ Sun, 21 Jun 2020 19:31:24: Done! pass1 - making usageList (526 chroms): 2 millis pass2 - checking and writing primary data (2120 records, 4 fields): 30 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:31:25: #2 number of paired peaks: 379 WARNING @ Sun, 21 Jun 2020 19:31:25: Fewer paired peaks (379) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 379 pairs to build model! INFO @ Sun, 21 Jun 2020 19:31:25: start model_add_line... INFO @ Sun, 21 Jun 2020 19:31:25: start X-correlation... INFO @ Sun, 21 Jun 2020 19:31:25: end of X-cor INFO @ Sun, 21 Jun 2020 19:31:25: #2 finished! INFO @ Sun, 21 Jun 2020 19:31:25: #2 predicted fragment length is 44 bps INFO @ Sun, 21 Jun 2020 19:31:25: #2 alternative fragment length(s) may be 4,44 bps INFO @ Sun, 21 Jun 2020 19:31:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287917/SRX287917.20_model.r WARNING @ Sun, 21 Jun 2020 19:31:25: #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 19:31:25: #2 You may need to consider one of the other alternative d(s): 4,44 WARNING @ Sun, 21 Jun 2020 19:31:25: #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 19:31:25: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:31:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:31:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287917/SRX287917.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:31:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287917/SRX287917.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:31:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287917/SRX287917.10_summits.bed INFO @ Sun, 21 Jun 2020 19:31:32: Done! pass1 - making usageList (451 chroms): 1 millis pass2 - checking and writing primary data (1564 records, 4 fields): 26 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:31:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:32:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287917/SRX287917.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:32:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287917/SRX287917.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:32:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287917/SRX287917.20_summits.bed INFO @ Sun, 21 Jun 2020 19:32:00: Done! pass1 - making usageList (259 chroms): 1 millis pass2 - checking and writing primary data (518 records, 4 fields): 16 millis CompletedMACS2peakCalling