Job ID = 6498025 SRX = SRX287898 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T23:06:04 prefetch.2.10.7: 1) Downloading 'SRR870087'... 2020-06-25T23:06:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T23:07:54 prefetch.2.10.7: HTTPS download succeed 2020-06-25T23:07:55 prefetch.2.10.7: 'SRR870087' is valid 2020-06-25T23:07:55 prefetch.2.10.7: 1) 'SRR870087' was downloaded successfully Read 13389851 spots for SRR870087/SRR870087.sra Written 13389851 spots for SRR870087/SRR870087.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: 00:05:15 13389851 reads; of these: 13389851 (100.00%) were unpaired; of these: 780789 (5.83%) aligned 0 times 8324668 (62.17%) aligned exactly 1 time 4284394 (32.00%) aligned >1 times 94.17% overall alignment rate Time searching: 00:05:15 Overall time: 00:05:15 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 1578700 / 12609062 = 0.1252 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 @ Fri, 26 Jun 2020 08:17:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287898/SRX287898.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287898/SRX287898.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287898/SRX287898.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287898/SRX287898.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 @ Fri, 26 Jun 2020 08:17:45: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:17:45: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:17:51: 1000000 INFO @ Fri, 26 Jun 2020 08:17:56: 2000000 INFO @ Fri, 26 Jun 2020 08:18:02: 3000000 INFO @ Fri, 26 Jun 2020 08:18:08: 4000000 INFO @ Fri, 26 Jun 2020 08:18:13: 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 @ Fri, 26 Jun 2020 08:18:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287898/SRX287898.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287898/SRX287898.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287898/SRX287898.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287898/SRX287898.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 @ Fri, 26 Jun 2020 08:18:15: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:18:15: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:18:19: 6000000 INFO @ Fri, 26 Jun 2020 08:18:22: 1000000 INFO @ Fri, 26 Jun 2020 08:18:25: 7000000 INFO @ Fri, 26 Jun 2020 08:18:28: 2000000 INFO @ Fri, 26 Jun 2020 08:18:31: 8000000 INFO @ Fri, 26 Jun 2020 08:18:34: 3000000 INFO @ Fri, 26 Jun 2020 08:18:36: 9000000 INFO @ Fri, 26 Jun 2020 08:18:41: 4000000 INFO @ Fri, 26 Jun 2020 08:18:42: 10000000 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 @ Fri, 26 Jun 2020 08:18:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287898/SRX287898.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287898/SRX287898.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287898/SRX287898.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287898/SRX287898.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 @ Fri, 26 Jun 2020 08:18:45: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:18:45: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:18:47: 5000000 INFO @ Fri, 26 Jun 2020 08:18:48: 11000000 INFO @ Fri, 26 Jun 2020 08:18:49: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:18:49: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:18:49: #1 total tags in treatment: 11030362 INFO @ Fri, 26 Jun 2020 08:18:49: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:18:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:18:49: #1 tags after filtering in treatment: 11030362 INFO @ Fri, 26 Jun 2020 08:18:49: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:18:49: #1 finished! INFO @ Fri, 26 Jun 2020 08:18:49: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:18:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:18:50: #2 number of paired peaks: 471 WARNING @ Fri, 26 Jun 2020 08:18:50: Fewer paired peaks (471) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 471 pairs to build model! INFO @ Fri, 26 Jun 2020 08:18:50: start model_add_line... INFO @ Fri, 26 Jun 2020 08:18:50: start X-correlation... INFO @ Fri, 26 Jun 2020 08:18:50: end of X-cor INFO @ Fri, 26 Jun 2020 08:18:50: #2 finished! INFO @ Fri, 26 Jun 2020 08:18:50: #2 predicted fragment length is 46 bps INFO @ Fri, 26 Jun 2020 08:18:50: #2 alternative fragment length(s) may be 46 bps INFO @ Fri, 26 Jun 2020 08:18:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287898/SRX287898.05_model.r WARNING @ Fri, 26 Jun 2020 08:18:50: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 08:18:50: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Fri, 26 Jun 2020 08:18:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 08:18:50: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:18:50: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:18:52: 1000000 INFO @ Fri, 26 Jun 2020 08:18:54: 6000000 INFO @ Fri, 26 Jun 2020 08:18:58: 2000000 INFO @ Fri, 26 Jun 2020 08:19:00: 7000000 INFO @ Fri, 26 Jun 2020 08:19:04: 3000000 INFO @ Fri, 26 Jun 2020 08:19:07: 8000000 INFO @ Fri, 26 Jun 2020 08:19:11: 4000000 INFO @ Fri, 26 Jun 2020 08:19:13: 9000000 INFO @ Fri, 26 Jun 2020 08:19:15: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:19:17: 5000000 INFO @ Fri, 26 Jun 2020 08:19:20: 10000000 INFO @ Fri, 26 Jun 2020 08:19:24: 6000000 INFO @ Fri, 26 Jun 2020 08:19:26: 11000000 INFO @ Fri, 26 Jun 2020 08:19:26: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:19:26: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:19:26: #1 total tags in treatment: 11030362 INFO @ Fri, 26 Jun 2020 08:19:26: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:19:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:19:27: #1 tags after filtering in treatment: 11030362 INFO @ Fri, 26 Jun 2020 08:19:27: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:19:27: #1 finished! INFO @ Fri, 26 Jun 2020 08:19:27: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:19:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:19:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287898/SRX287898.05_peaks.xls INFO @ Fri, 26 Jun 2020 08:19:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287898/SRX287898.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:19:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287898/SRX287898.05_summits.bed INFO @ Fri, 26 Jun 2020 08:19:27: Done! INFO @ Fri, 26 Jun 2020 08:19:27: #2 number of paired peaks: 471 WARNING @ Fri, 26 Jun 2020 08:19:27: Fewer paired peaks (471) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 471 pairs to build model! INFO @ Fri, 26 Jun 2020 08:19:27: start model_add_line... INFO @ Fri, 26 Jun 2020 08:19:28: start X-correlation... INFO @ Fri, 26 Jun 2020 08:19:28: end of X-cor INFO @ Fri, 26 Jun 2020 08:19:28: #2 finished! INFO @ Fri, 26 Jun 2020 08:19:28: #2 predicted fragment length is 46 bps INFO @ Fri, 26 Jun 2020 08:19:28: #2 alternative fragment length(s) may be 46 bps INFO @ Fri, 26 Jun 2020 08:19:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287898/SRX287898.10_model.r WARNING @ Fri, 26 Jun 2020 08:19:28: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 08:19:28: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Fri, 26 Jun 2020 08:19:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 08:19:28: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:19:28: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (2050 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:19:30: 7000000 INFO @ Fri, 26 Jun 2020 08:19:36: 8000000 INFO @ Fri, 26 Jun 2020 08:19:43: 9000000 INFO @ Fri, 26 Jun 2020 08:19:49: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 08:19:52: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:19:55: 11000000 INFO @ Fri, 26 Jun 2020 08:19:55: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:19:55: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:19:55: #1 total tags in treatment: 11030362 INFO @ Fri, 26 Jun 2020 08:19:55: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:19:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:19:55: #1 tags after filtering in treatment: 11030362 INFO @ Fri, 26 Jun 2020 08:19:55: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:19:55: #1 finished! INFO @ Fri, 26 Jun 2020 08:19:55: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:19:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:19:56: #2 number of paired peaks: 471 WARNING @ Fri, 26 Jun 2020 08:19:56: Fewer paired peaks (471) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 471 pairs to build model! INFO @ Fri, 26 Jun 2020 08:19:56: start model_add_line... INFO @ Fri, 26 Jun 2020 08:19:56: start X-correlation... INFO @ Fri, 26 Jun 2020 08:19:56: end of X-cor INFO @ Fri, 26 Jun 2020 08:19:56: #2 finished! INFO @ Fri, 26 Jun 2020 08:19:56: #2 predicted fragment length is 46 bps INFO @ Fri, 26 Jun 2020 08:19:56: #2 alternative fragment length(s) may be 46 bps INFO @ Fri, 26 Jun 2020 08:19:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287898/SRX287898.20_model.r WARNING @ Fri, 26 Jun 2020 08:19:56: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 08:19:56: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Fri, 26 Jun 2020 08:19:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 08:19:56: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:19:56: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:20:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287898/SRX287898.10_peaks.xls INFO @ Fri, 26 Jun 2020 08:20:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287898/SRX287898.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:20:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287898/SRX287898.10_summits.bed INFO @ Fri, 26 Jun 2020 08:20:05: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1767 records, 4 fields): 4 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 08:20:21: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:20:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287898/SRX287898.20_peaks.xls INFO @ Fri, 26 Jun 2020 08:20:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287898/SRX287898.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:20:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287898/SRX287898.20_summits.bed INFO @ Fri, 26 Jun 2020 08:20:33: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1335 records, 4 fields): 3 millis CompletedMACS2peakCalling