Job ID = 6369032 SRX = SRX982097 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:42:27 prefetch.2.10.7: 1) Downloading 'SRR1956584'... 2020-06-16T00:42:27 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:46:38 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:46:39 prefetch.2.10.7: 'SRR1956584' is valid 2020-06-16T00:46:39 prefetch.2.10.7: 1) 'SRR1956584' was downloaded successfully Read 11412023 spots for SRR1956584/SRR1956584.sra Written 11412023 spots for SRR1956584/SRR1956584.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: 00:03:37 11412023 reads; of these: 11412023 (100.00%) were unpaired; of these: 306660 (2.69%) aligned 0 times 9367907 (82.09%) aligned exactly 1 time 1737456 (15.22%) aligned >1 times 97.31% overall alignment rate Time searching: 00:03:37 Overall time: 00:03:37 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] 2913597 / 11105363 = 0.2624 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 09:54:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982097/SRX982097.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982097/SRX982097.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982097/SRX982097.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982097/SRX982097.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 09:54:46: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:54:46: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:54:52: 1000000 INFO @ Tue, 16 Jun 2020 09:54:59: 2000000 INFO @ Tue, 16 Jun 2020 09:55:06: 3000000 INFO @ Tue, 16 Jun 2020 09:55:12: 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 09:55:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982097/SRX982097.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982097/SRX982097.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982097/SRX982097.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982097/SRX982097.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 09:55:16: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:55:16: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:55:20: 5000000 INFO @ Tue, 16 Jun 2020 09:55:25: 1000000 INFO @ Tue, 16 Jun 2020 09:55:28: 6000000 INFO @ Tue, 16 Jun 2020 09:55:34: 2000000 INFO @ Tue, 16 Jun 2020 09:55:37: 7000000 INFO @ Tue, 16 Jun 2020 09:55:43: 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 @ Tue, 16 Jun 2020 09:55:45: 8000000 INFO @ Tue, 16 Jun 2020 09:55:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982097/SRX982097.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982097/SRX982097.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982097/SRX982097.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982097/SRX982097.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 09:55:46: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:55:46: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:55:47: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:55:47: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:55:47: #1 total tags in treatment: 8191766 INFO @ Tue, 16 Jun 2020 09:55:47: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:55:47: #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 09:55:47: #1 tags after filtering in treatment: 8191766 INFO @ Tue, 16 Jun 2020 09:55:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:55:47: #1 finished! INFO @ Tue, 16 Jun 2020 09:55:47: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:55:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:55:47: #2 number of paired peaks: 351 WARNING @ Tue, 16 Jun 2020 09:55:47: Fewer paired peaks (351) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 351 pairs to build model! INFO @ Tue, 16 Jun 2020 09:55:47: start model_add_line... INFO @ Tue, 16 Jun 2020 09:55:48: start X-correlation... INFO @ Tue, 16 Jun 2020 09:55:48: end of X-cor INFO @ Tue, 16 Jun 2020 09:55:48: #2 finished! INFO @ Tue, 16 Jun 2020 09:55:48: #2 predicted fragment length is 74 bps INFO @ Tue, 16 Jun 2020 09:55:48: #2 alternative fragment length(s) may be 4,74 bps INFO @ Tue, 16 Jun 2020 09:55:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982097/SRX982097.05_model.r WARNING @ Tue, 16 Jun 2020 09:55:48: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:55:48: #2 You may need to consider one of the other alternative d(s): 4,74 WARNING @ Tue, 16 Jun 2020 09:55:48: #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 09:55:48: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:55:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:55:52: 4000000 INFO @ Tue, 16 Jun 2020 09:55:55: 1000000 INFO @ Tue, 16 Jun 2020 09:56:01: 5000000 INFO @ Tue, 16 Jun 2020 09:56:03: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:56:04: 2000000 INFO @ Tue, 16 Jun 2020 09:56:11: 6000000 INFO @ Tue, 16 Jun 2020 09:56:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982097/SRX982097.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:56:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982097/SRX982097.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:56:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982097/SRX982097.05_summits.bed INFO @ Tue, 16 Jun 2020 09:56:11: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (526 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:56:14: 3000000 INFO @ Tue, 16 Jun 2020 09:56:20: 7000000 INFO @ Tue, 16 Jun 2020 09:56:23: 4000000 INFO @ Tue, 16 Jun 2020 09:56:30: 8000000 INFO @ Tue, 16 Jun 2020 09:56:31: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:56:31: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:56:31: #1 total tags in treatment: 8191766 INFO @ Tue, 16 Jun 2020 09:56:31: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:56:31: #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 09:56:31: #1 tags after filtering in treatment: 8191766 INFO @ Tue, 16 Jun 2020 09:56:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:56:31: #1 finished! INFO @ Tue, 16 Jun 2020 09:56:31: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:56:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:56:32: #2 number of paired peaks: 351 WARNING @ Tue, 16 Jun 2020 09:56:32: Fewer paired peaks (351) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 351 pairs to build model! INFO @ Tue, 16 Jun 2020 09:56:32: start model_add_line... INFO @ Tue, 16 Jun 2020 09:56:32: start X-correlation... INFO @ Tue, 16 Jun 2020 09:56:32: end of X-cor INFO @ Tue, 16 Jun 2020 09:56:32: #2 finished! INFO @ Tue, 16 Jun 2020 09:56:32: #2 predicted fragment length is 74 bps INFO @ Tue, 16 Jun 2020 09:56:32: #2 alternative fragment length(s) may be 4,74 bps INFO @ Tue, 16 Jun 2020 09:56:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982097/SRX982097.10_model.r WARNING @ Tue, 16 Jun 2020 09:56:32: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:56:32: #2 You may need to consider one of the other alternative d(s): 4,74 WARNING @ Tue, 16 Jun 2020 09:56:32: #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 09:56:32: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:56:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:56:33: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:56:41: 6000000 INFO @ Tue, 16 Jun 2020 09:56:49: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:56:50: 7000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:56:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982097/SRX982097.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:56:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982097/SRX982097.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:56:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982097/SRX982097.10_summits.bed INFO @ Tue, 16 Jun 2020 09:56:57: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (388 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:56:59: 8000000 INFO @ Tue, 16 Jun 2020 09:57:00: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:57:00: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:57:00: #1 total tags in treatment: 8191766 INFO @ Tue, 16 Jun 2020 09:57:00: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:57:00: #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 09:57:00: #1 tags after filtering in treatment: 8191766 INFO @ Tue, 16 Jun 2020 09:57:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:57:00: #1 finished! INFO @ Tue, 16 Jun 2020 09:57:00: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:57:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:57:01: #2 number of paired peaks: 351 WARNING @ Tue, 16 Jun 2020 09:57:01: Fewer paired peaks (351) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 351 pairs to build model! INFO @ Tue, 16 Jun 2020 09:57:01: start model_add_line... INFO @ Tue, 16 Jun 2020 09:57:01: start X-correlation... INFO @ Tue, 16 Jun 2020 09:57:01: end of X-cor INFO @ Tue, 16 Jun 2020 09:57:01: #2 finished! INFO @ Tue, 16 Jun 2020 09:57:01: #2 predicted fragment length is 74 bps INFO @ Tue, 16 Jun 2020 09:57:01: #2 alternative fragment length(s) may be 4,74 bps INFO @ Tue, 16 Jun 2020 09:57:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982097/SRX982097.20_model.r WARNING @ Tue, 16 Jun 2020 09:57:01: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:57:01: #2 You may need to consider one of the other alternative d(s): 4,74 WARNING @ Tue, 16 Jun 2020 09:57:01: #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 09:57:01: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:57:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:57:18: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:57:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982097/SRX982097.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:57:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982097/SRX982097.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:57:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982097/SRX982097.20_summits.bed INFO @ Tue, 16 Jun 2020 09:57:26: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (217 records, 4 fields): 1 millis CompletedMACS2peakCalling