Job ID = 6367591 SRX = SRX331348 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:29:50 prefetch.2.10.7: 1) Downloading 'SRR947585'... 2020-06-15T23:29:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:32:31 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:32:32 prefetch.2.10.7: 'SRR947585' is valid 2020-06-15T23:32:32 prefetch.2.10.7: 1) 'SRR947585' was downloaded successfully Read 13598392 spots for SRR947585/SRR947585.sra Written 13598392 spots for SRR947585/SRR947585.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: 00:02:57 13598392 reads; of these: 13598392 (100.00%) were unpaired; of these: 978141 (7.19%) aligned 0 times 10971906 (80.69%) aligned exactly 1 time 1648345 (12.12%) aligned >1 times 92.81% overall alignment rate Time searching: 00:02:57 Overall time: 00:02:57 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 8 files... [bam_rmdupse_core] 6982461 / 12620251 = 0.5533 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 08:38:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331348/SRX331348.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331348/SRX331348.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331348/SRX331348.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331348/SRX331348.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 08:38:57: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:38:57: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:39:03: 1000000 INFO @ Tue, 16 Jun 2020 08:39:10: 2000000 INFO @ Tue, 16 Jun 2020 08:39:16: 3000000 INFO @ Tue, 16 Jun 2020 08:39:23: 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 08:39:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331348/SRX331348.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331348/SRX331348.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331348/SRX331348.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331348/SRX331348.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 08:39:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:39:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:39:30: 5000000 INFO @ Tue, 16 Jun 2020 08:39:33: 1000000 INFO @ Tue, 16 Jun 2020 08:39:34: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:39:34: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:39:34: #1 total tags in treatment: 5637790 INFO @ Tue, 16 Jun 2020 08:39:34: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:39:34: #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 08:39:34: #1 tags after filtering in treatment: 5637790 INFO @ Tue, 16 Jun 2020 08:39:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:39:34: #1 finished! INFO @ Tue, 16 Jun 2020 08:39:34: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:39:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:39:34: #2 number of paired peaks: 523 WARNING @ Tue, 16 Jun 2020 08:39:34: Fewer paired peaks (523) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 523 pairs to build model! INFO @ Tue, 16 Jun 2020 08:39:34: start model_add_line... INFO @ Tue, 16 Jun 2020 08:39:34: start X-correlation... INFO @ Tue, 16 Jun 2020 08:39:34: end of X-cor INFO @ Tue, 16 Jun 2020 08:39:34: #2 finished! INFO @ Tue, 16 Jun 2020 08:39:34: #2 predicted fragment length is 53 bps INFO @ Tue, 16 Jun 2020 08:39:34: #2 alternative fragment length(s) may be 4,53,579 bps INFO @ Tue, 16 Jun 2020 08:39:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331348/SRX331348.05_model.r WARNING @ Tue, 16 Jun 2020 08:39:34: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:39:34: #2 You may need to consider one of the other alternative d(s): 4,53,579 WARNING @ Tue, 16 Jun 2020 08:39:34: #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 08:39:34: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:39:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:39:39: 2000000 INFO @ Tue, 16 Jun 2020 08:39:45: 3000000 INFO @ Tue, 16 Jun 2020 08:39:46: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:39:51: 4000000 INFO @ Tue, 16 Jun 2020 08:39:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331348/SRX331348.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:39:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331348/SRX331348.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:39:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331348/SRX331348.05_summits.bed INFO @ Tue, 16 Jun 2020 08:39:52: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1013 records, 4 fields): 3 millis CompletedMACS2peakCalling 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 08:39:57: 5000000 INFO @ Tue, 16 Jun 2020 08:39:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX331348/SRX331348.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX331348/SRX331348.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX331348/SRX331348.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX331348/SRX331348.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 08:39:57: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:39:57: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:40:00: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:40:00: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:40:00: #1 total tags in treatment: 5637790 INFO @ Tue, 16 Jun 2020 08:40:00: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:40:00: #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 08:40:01: #1 tags after filtering in treatment: 5637790 INFO @ Tue, 16 Jun 2020 08:40:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:40:01: #1 finished! INFO @ Tue, 16 Jun 2020 08:40:01: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:40:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:40:01: #2 number of paired peaks: 523 WARNING @ Tue, 16 Jun 2020 08:40:01: Fewer paired peaks (523) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 523 pairs to build model! INFO @ Tue, 16 Jun 2020 08:40:01: start model_add_line... INFO @ Tue, 16 Jun 2020 08:40:01: start X-correlation... INFO @ Tue, 16 Jun 2020 08:40:01: end of X-cor INFO @ Tue, 16 Jun 2020 08:40:01: #2 finished! INFO @ Tue, 16 Jun 2020 08:40:01: #2 predicted fragment length is 53 bps INFO @ Tue, 16 Jun 2020 08:40:01: #2 alternative fragment length(s) may be 4,53,579 bps INFO @ Tue, 16 Jun 2020 08:40:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331348/SRX331348.10_model.r WARNING @ Tue, 16 Jun 2020 08:40:01: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:40:01: #2 You may need to consider one of the other alternative d(s): 4,53,579 WARNING @ Tue, 16 Jun 2020 08:40:01: #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 08:40:01: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:40:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:40:04: 1000000 INFO @ Tue, 16 Jun 2020 08:40:11: 2000000 INFO @ Tue, 16 Jun 2020 08:40:13: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:40:18: 3000000 INFO @ Tue, 16 Jun 2020 08:40:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331348/SRX331348.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:40:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331348/SRX331348.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:40:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331348/SRX331348.10_summits.bed INFO @ Tue, 16 Jun 2020 08:40:19: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (388 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:40:24: 4000000 INFO @ Tue, 16 Jun 2020 08:40:31: 5000000 INFO @ Tue, 16 Jun 2020 08:40:35: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:40:35: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:40:35: #1 total tags in treatment: 5637790 INFO @ Tue, 16 Jun 2020 08:40:35: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:40:35: #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 08:40:35: #1 tags after filtering in treatment: 5637790 INFO @ Tue, 16 Jun 2020 08:40:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:40:35: #1 finished! INFO @ Tue, 16 Jun 2020 08:40:35: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:40:35: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:40:35: #2 number of paired peaks: 523 WARNING @ Tue, 16 Jun 2020 08:40:35: Fewer paired peaks (523) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 523 pairs to build model! INFO @ Tue, 16 Jun 2020 08:40:35: start model_add_line... INFO @ Tue, 16 Jun 2020 08:40:35: start X-correlation... INFO @ Tue, 16 Jun 2020 08:40:36: end of X-cor INFO @ Tue, 16 Jun 2020 08:40:36: #2 finished! INFO @ Tue, 16 Jun 2020 08:40:36: #2 predicted fragment length is 53 bps INFO @ Tue, 16 Jun 2020 08:40:36: #2 alternative fragment length(s) may be 4,53,579 bps INFO @ Tue, 16 Jun 2020 08:40:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX331348/SRX331348.20_model.r WARNING @ Tue, 16 Jun 2020 08:40:36: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:40:36: #2 You may need to consider one of the other alternative d(s): 4,53,579 WARNING @ Tue, 16 Jun 2020 08:40:36: #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 08:40:36: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:40:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:40:47: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:40:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX331348/SRX331348.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:40:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX331348/SRX331348.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:40:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX331348/SRX331348.20_summits.bed INFO @ Tue, 16 Jun 2020 08:40:54: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (127 records, 4 fields): 1 millis CompletedMACS2peakCalling