Job ID = 6368589 SRX = SRX5020815 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:27:01 prefetch.2.10.7: 1) Downloading 'SRR8201438'... 2020-06-16T00:27:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:28:41 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:28:41 prefetch.2.10.7: 'SRR8201438' is valid 2020-06-16T00:28:41 prefetch.2.10.7: 1) 'SRR8201438' was downloaded successfully Read 10633946 spots for SRR8201438/SRR8201438.sra Written 10633946 spots for SRR8201438/SRR8201438.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: 00:02:36 10633946 reads; of these: 10633946 (100.00%) were unpaired; of these: 136488 (1.28%) aligned 0 times 8689873 (81.72%) aligned exactly 1 time 1807585 (17.00%) aligned >1 times 98.72% overall alignment rate Time searching: 00:02:36 Overall time: 00:02:36 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] 746063 / 10497458 = 0.0711 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 09:35:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020815/SRX5020815.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020815/SRX5020815.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020815/SRX5020815.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020815/SRX5020815.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 09:35:12: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:35:12: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:35:19: 1000000 INFO @ Tue, 16 Jun 2020 09:35:27: 2000000 INFO @ Tue, 16 Jun 2020 09:35:34: 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 @ Tue, 16 Jun 2020 09:35:41: 4000000 INFO @ Tue, 16 Jun 2020 09:35:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020815/SRX5020815.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020815/SRX5020815.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020815/SRX5020815.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020815/SRX5020815.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 09:35:42: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:35:42: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:35:49: 5000000 INFO @ Tue, 16 Jun 2020 09:35:49: 1000000 INFO @ Tue, 16 Jun 2020 09:35:57: 2000000 INFO @ Tue, 16 Jun 2020 09:35:57: 6000000 INFO @ Tue, 16 Jun 2020 09:36:04: 3000000 INFO @ Tue, 16 Jun 2020 09:36:05: 7000000 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 09:36:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020815/SRX5020815.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020815/SRX5020815.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020815/SRX5020815.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020815/SRX5020815.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 09:36:12: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:36:12: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:36:12: 4000000 INFO @ Tue, 16 Jun 2020 09:36:13: 8000000 INFO @ Tue, 16 Jun 2020 09:36:19: 5000000 INFO @ Tue, 16 Jun 2020 09:36:20: 1000000 INFO @ Tue, 16 Jun 2020 09:36:21: 9000000 INFO @ Tue, 16 Jun 2020 09:36:27: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:36:27: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:36:27: #1 total tags in treatment: 9751395 INFO @ Tue, 16 Jun 2020 09:36:27: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:36:27: #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 09:36:27: 6000000 INFO @ Tue, 16 Jun 2020 09:36:27: #1 tags after filtering in treatment: 9751395 INFO @ Tue, 16 Jun 2020 09:36:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:36:27: #1 finished! INFO @ Tue, 16 Jun 2020 09:36:27: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:36:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:36:28: #2 number of paired peaks: 321 WARNING @ Tue, 16 Jun 2020 09:36:28: Fewer paired peaks (321) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 321 pairs to build model! INFO @ Tue, 16 Jun 2020 09:36:28: start model_add_line... INFO @ Tue, 16 Jun 2020 09:36:28: start X-correlation... INFO @ Tue, 16 Jun 2020 09:36:28: end of X-cor INFO @ Tue, 16 Jun 2020 09:36:28: #2 finished! INFO @ Tue, 16 Jun 2020 09:36:28: #2 predicted fragment length is 44 bps INFO @ Tue, 16 Jun 2020 09:36:28: #2 alternative fragment length(s) may be 3,44 bps INFO @ Tue, 16 Jun 2020 09:36:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020815/SRX5020815.05_model.r WARNING @ Tue, 16 Jun 2020 09:36:28: #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 09:36:28: #2 You may need to consider one of the other alternative d(s): 3,44 WARNING @ Tue, 16 Jun 2020 09:36:28: #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 09:36:28: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:36:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:36:29: 2000000 INFO @ Tue, 16 Jun 2020 09:36:34: 7000000 INFO @ Tue, 16 Jun 2020 09:36:37: 3000000 INFO @ Tue, 16 Jun 2020 09:36:42: 8000000 INFO @ Tue, 16 Jun 2020 09:36:45: 4000000 INFO @ Tue, 16 Jun 2020 09:36:46: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:36:49: 9000000 INFO @ Tue, 16 Jun 2020 09:36:54: 5000000 INFO @ Tue, 16 Jun 2020 09:36:55: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:36:55: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:36:55: #1 total tags in treatment: 9751395 INFO @ Tue, 16 Jun 2020 09:36:55: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:36:55: #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 09:36:55: #1 tags after filtering in treatment: 9751395 INFO @ Tue, 16 Jun 2020 09:36:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:36:55: #1 finished! INFO @ Tue, 16 Jun 2020 09:36:55: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:36:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:36:55: #2 number of paired peaks: 321 WARNING @ Tue, 16 Jun 2020 09:36:55: Fewer paired peaks (321) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 321 pairs to build model! INFO @ Tue, 16 Jun 2020 09:36:55: start model_add_line... INFO @ Tue, 16 Jun 2020 09:36:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020815/SRX5020815.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:36:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020815/SRX5020815.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:36:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020815/SRX5020815.05_summits.bed INFO @ Tue, 16 Jun 2020 09:36:55: Done! INFO @ Tue, 16 Jun 2020 09:36:55: start X-correlation... INFO @ Tue, 16 Jun 2020 09:36:56: end of X-cor INFO @ Tue, 16 Jun 2020 09:36:56: #2 finished! INFO @ Tue, 16 Jun 2020 09:36:56: #2 predicted fragment length is 44 bps INFO @ Tue, 16 Jun 2020 09:36:56: #2 alternative fragment length(s) may be 3,44 bps INFO @ Tue, 16 Jun 2020 09:36:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020815/SRX5020815.10_model.r WARNING @ Tue, 16 Jun 2020 09:36:56: #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 09:36:56: #2 You may need to consider one of the other alternative d(s): 3,44 WARNING @ Tue, 16 Jun 2020 09:36:56: #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 09:36:56: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:36:56: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (646 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:37:02: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:37:09: 7000000 INFO @ Tue, 16 Jun 2020 09:37:14: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:37:17: 8000000 INFO @ Tue, 16 Jun 2020 09:37:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020815/SRX5020815.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:37:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020815/SRX5020815.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:37:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020815/SRX5020815.10_summits.bed INFO @ Tue, 16 Jun 2020 09:37:23: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (397 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:37:24: 9000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:37:30: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:37:30: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:37:30: #1 total tags in treatment: 9751395 INFO @ Tue, 16 Jun 2020 09:37:30: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:37:30: #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 09:37:30: #1 tags after filtering in treatment: 9751395 INFO @ Tue, 16 Jun 2020 09:37:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:37:30: #1 finished! INFO @ Tue, 16 Jun 2020 09:37:30: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:37:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:37:30: #2 number of paired peaks: 321 WARNING @ Tue, 16 Jun 2020 09:37:30: Fewer paired peaks (321) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 321 pairs to build model! INFO @ Tue, 16 Jun 2020 09:37:30: start model_add_line... INFO @ Tue, 16 Jun 2020 09:37:31: start X-correlation... INFO @ Tue, 16 Jun 2020 09:37:31: end of X-cor INFO @ Tue, 16 Jun 2020 09:37:31: #2 finished! INFO @ Tue, 16 Jun 2020 09:37:31: #2 predicted fragment length is 44 bps INFO @ Tue, 16 Jun 2020 09:37:31: #2 alternative fragment length(s) may be 3,44 bps INFO @ Tue, 16 Jun 2020 09:37:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020815/SRX5020815.20_model.r WARNING @ Tue, 16 Jun 2020 09:37:31: #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 09:37:31: #2 You may need to consider one of the other alternative d(s): 3,44 WARNING @ Tue, 16 Jun 2020 09:37:31: #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 09:37:31: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:37:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:37:50: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:37:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020815/SRX5020815.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:37:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020815/SRX5020815.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:37:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020815/SRX5020815.20_summits.bed INFO @ Tue, 16 Jun 2020 09:37:59: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (152 records, 4 fields): 1 millis CompletedMACS2peakCalling