Job ID = 6367589 SRX = SRX331346 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:31:35 prefetch.2.10.7: 1) Downloading 'SRR947583'... 2020-06-15T23:31:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:34:07 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:34:07 prefetch.2.10.7: 1) 'SRR947583' was downloaded successfully Read 22858982 spots for SRR947583/SRR947583.sra Written 22858982 spots for SRR947583/SRR947583.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: 00:04:50 22858982 reads; of these: 22858982 (100.00%) were unpaired; of these: 654294 (2.86%) aligned 0 times 18698509 (81.80%) aligned exactly 1 time 3506179 (15.34%) aligned >1 times 97.14% overall alignment rate Time searching: 00:04:50 Overall time: 00:04:50 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 8948023 / 22204688 = 0.4030 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 @ Tue, 16 Jun 2020 08:44:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331346/SRX331346.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331346/SRX331346.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331346/SRX331346.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331346/SRX331346.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 16 Jun 2020 08:44:51: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:44:51: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:44:57: 1000000 INFO @ Tue, 16 Jun 2020 08:45:02: 2000000 INFO @ Tue, 16 Jun 2020 08:45:08: 3000000 INFO @ Tue, 16 Jun 2020 08:45:14: 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 @ Tue, 16 Jun 2020 08:45:20: 5000000 INFO @ Tue, 16 Jun 2020 08:45:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331346/SRX331346.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331346/SRX331346.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331346/SRX331346.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331346/SRX331346.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 16 Jun 2020 08:45:21: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:45:21: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:45:26: 6000000 INFO @ Tue, 16 Jun 2020 08:45:28: 1000000 INFO @ Tue, 16 Jun 2020 08:45:33: 7000000 INFO @ Tue, 16 Jun 2020 08:45:34: 2000000 INFO @ Tue, 16 Jun 2020 08:45:39: 8000000 INFO @ Tue, 16 Jun 2020 08:45:41: 3000000 INFO @ Tue, 16 Jun 2020 08:45:46: 9000000 INFO @ Tue, 16 Jun 2020 08:45:47: 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 @ Tue, 16 Jun 2020 08:45:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331346/SRX331346.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331346/SRX331346.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331346/SRX331346.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331346/SRX331346.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 16 Jun 2020 08:45:51: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:45:51: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:45:52: 10000000 INFO @ Tue, 16 Jun 2020 08:45:54: 5000000 INFO @ Tue, 16 Jun 2020 08:45:58: 1000000 INFO @ Tue, 16 Jun 2020 08:45:59: 11000000 INFO @ Tue, 16 Jun 2020 08:46:01: 6000000 INFO @ Tue, 16 Jun 2020 08:46:05: 2000000 INFO @ Tue, 16 Jun 2020 08:46:06: 12000000 INFO @ Tue, 16 Jun 2020 08:46:08: 7000000 INFO @ Tue, 16 Jun 2020 08:46:11: 3000000 INFO @ Tue, 16 Jun 2020 08:46:13: 13000000 INFO @ Tue, 16 Jun 2020 08:46:15: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:46:15: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:46:15: #1 total tags in treatment: 13256665 INFO @ Tue, 16 Jun 2020 08:46:15: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:46:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:46:15: #1 tags after filtering in treatment: 13256665 INFO @ Tue, 16 Jun 2020 08:46:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:46:15: #1 finished! INFO @ Tue, 16 Jun 2020 08:46:15: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:46:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:46:15: 8000000 INFO @ Tue, 16 Jun 2020 08:46:16: #2 number of paired peaks: 325 WARNING @ Tue, 16 Jun 2020 08:46:16: Fewer paired peaks (325) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 325 pairs to build model! INFO @ Tue, 16 Jun 2020 08:46:16: start model_add_line... INFO @ Tue, 16 Jun 2020 08:46:16: start X-correlation... INFO @ Tue, 16 Jun 2020 08:46:16: end of X-cor INFO @ Tue, 16 Jun 2020 08:46:16: #2 finished! INFO @ Tue, 16 Jun 2020 08:46:16: #2 predicted fragment length is 44 bps INFO @ Tue, 16 Jun 2020 08:46:16: #2 alternative fragment length(s) may be 1,44,558,573 bps INFO @ Tue, 16 Jun 2020 08:46:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331346/SRX331346.05_model.r WARNING @ Tue, 16 Jun 2020 08:46:16: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:46:16: #2 You may need to consider one of the other alternative d(s): 1,44,558,573 WARNING @ Tue, 16 Jun 2020 08:46:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:46:16: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:46:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:46:18: 4000000 INFO @ Tue, 16 Jun 2020 08:46:21: 9000000 INFO @ Tue, 16 Jun 2020 08:46:25: 5000000 INFO @ Tue, 16 Jun 2020 08:46:28: 10000000 INFO @ Tue, 16 Jun 2020 08:46:31: 6000000 INFO @ Tue, 16 Jun 2020 08:46:35: 11000000 INFO @ Tue, 16 Jun 2020 08:46:38: 7000000 INFO @ Tue, 16 Jun 2020 08:46:39: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:46:41: 12000000 INFO @ Tue, 16 Jun 2020 08:46:44: 8000000 INFO @ Tue, 16 Jun 2020 08:46:48: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:46:50: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:46:50: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:46:50: #1 total tags in treatment: 13256665 INFO @ Tue, 16 Jun 2020 08:46:50: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:46:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:46:50: #1 tags after filtering in treatment: 13256665 INFO @ Tue, 16 Jun 2020 08:46:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:46:50: #1 finished! INFO @ Tue, 16 Jun 2020 08:46:50: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:46:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:46:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331346/SRX331346.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:46:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331346/SRX331346.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:46:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331346/SRX331346.05_summits.bed INFO @ Tue, 16 Jun 2020 08:46:50: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (763 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:46:51: #2 number of paired peaks: 325 WARNING @ Tue, 16 Jun 2020 08:46:51: Fewer paired peaks (325) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 325 pairs to build model! INFO @ Tue, 16 Jun 2020 08:46:51: start model_add_line... INFO @ Tue, 16 Jun 2020 08:46:51: start X-correlation... INFO @ Tue, 16 Jun 2020 08:46:51: end of X-cor INFO @ Tue, 16 Jun 2020 08:46:51: #2 finished! INFO @ Tue, 16 Jun 2020 08:46:51: #2 predicted fragment length is 44 bps INFO @ Tue, 16 Jun 2020 08:46:51: #2 alternative fragment length(s) may be 1,44,558,573 bps INFO @ Tue, 16 Jun 2020 08:46:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331346/SRX331346.10_model.r WARNING @ Tue, 16 Jun 2020 08:46:51: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:46:51: #2 You may need to consider one of the other alternative d(s): 1,44,558,573 WARNING @ Tue, 16 Jun 2020 08:46:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:46:51: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:46:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:46:51: 9000000 INFO @ Tue, 16 Jun 2020 08:46:57: 10000000 INFO @ Tue, 16 Jun 2020 08:47:03: 11000000 INFO @ Tue, 16 Jun 2020 08:47:09: 12000000 INFO @ Tue, 16 Jun 2020 08:47:14: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:47:15: 13000000 INFO @ Tue, 16 Jun 2020 08:47:16: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:47:16: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:47:16: #1 total tags in treatment: 13256665 INFO @ Tue, 16 Jun 2020 08:47:16: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:47:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:47:16: #1 tags after filtering in treatment: 13256665 INFO @ Tue, 16 Jun 2020 08:47:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:47:16: #1 finished! INFO @ Tue, 16 Jun 2020 08:47:16: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:47:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:47:17: #2 number of paired peaks: 325 WARNING @ Tue, 16 Jun 2020 08:47:17: Fewer paired peaks (325) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 325 pairs to build model! INFO @ Tue, 16 Jun 2020 08:47:17: start model_add_line... INFO @ Tue, 16 Jun 2020 08:47:17: start X-correlation... INFO @ Tue, 16 Jun 2020 08:47:17: end of X-cor INFO @ Tue, 16 Jun 2020 08:47:17: #2 finished! INFO @ Tue, 16 Jun 2020 08:47:17: #2 predicted fragment length is 44 bps INFO @ Tue, 16 Jun 2020 08:47:17: #2 alternative fragment length(s) may be 1,44,558,573 bps INFO @ Tue, 16 Jun 2020 08:47:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331346/SRX331346.20_model.r WARNING @ Tue, 16 Jun 2020 08:47:17: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:47:17: #2 You may need to consider one of the other alternative d(s): 1,44,558,573 WARNING @ Tue, 16 Jun 2020 08:47:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:47:17: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:47:17: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:47:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331346/SRX331346.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:47:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331346/SRX331346.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:47:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331346/SRX331346.10_summits.bed INFO @ Tue, 16 Jun 2020 08:47:26: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (453 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:47:41: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:47:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331346/SRX331346.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:47:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331346/SRX331346.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:47:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331346/SRX331346.20_summits.bed INFO @ Tue, 16 Jun 2020 08:47:53: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (157 records, 4 fields): 1 millis CompletedMACS2peakCalling