Job ID = 6368515 SRX = SRX5020744 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:17:36 prefetch.2.10.7: 1) Downloading 'SRR8201367'... 2020-06-16T00:17:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:20:36 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:20:36 prefetch.2.10.7: 1) 'SRR8201367' was downloaded successfully 2020-06-16T00:20:36 prefetch.2.10.7: 'SRR8201367' has 0 unresolved dependencies Read 20115882 spots for SRR8201367/SRR8201367.sra Written 20115882 spots for SRR8201367/SRR8201367.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: 00:06:26 20115882 reads; of these: 20115882 (100.00%) were unpaired; of these: 234443 (1.17%) aligned 0 times 15615461 (77.63%) aligned exactly 1 time 4265978 (21.21%) aligned >1 times 98.83% overall alignment rate Time searching: 00:06:26 Overall time: 00:06:26 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] 2957511 / 19881439 = 0.1488 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 09:33:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020744/SRX5020744.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020744/SRX5020744.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020744/SRX5020744.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020744/SRX5020744.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 09:33:24: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:33:24: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:33:30: 1000000 INFO @ Tue, 16 Jun 2020 09:33:36: 2000000 INFO @ Tue, 16 Jun 2020 09:33:42: 3000000 INFO @ Tue, 16 Jun 2020 09:33:48: 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 09:33:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020744/SRX5020744.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020744/SRX5020744.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020744/SRX5020744.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020744/SRX5020744.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 09:33:54: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:33:54: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:33:55: 5000000 INFO @ Tue, 16 Jun 2020 09:34:00: 1000000 INFO @ Tue, 16 Jun 2020 09:34:01: 6000000 INFO @ Tue, 16 Jun 2020 09:34:06: 2000000 INFO @ Tue, 16 Jun 2020 09:34:07: 7000000 INFO @ Tue, 16 Jun 2020 09:34:14: 3000000 INFO @ Tue, 16 Jun 2020 09:34:15: 8000000 INFO @ Tue, 16 Jun 2020 09:34:20: 4000000 INFO @ Tue, 16 Jun 2020 09:34:21: 9000000 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 09:34:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020744/SRX5020744.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020744/SRX5020744.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020744/SRX5020744.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020744/SRX5020744.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 09:34:24: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:34:24: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:34:27: 5000000 INFO @ Tue, 16 Jun 2020 09:34:27: 10000000 INFO @ Tue, 16 Jun 2020 09:34:30: 1000000 INFO @ Tue, 16 Jun 2020 09:34:33: 6000000 INFO @ Tue, 16 Jun 2020 09:34:33: 11000000 INFO @ Tue, 16 Jun 2020 09:34:35: 2000000 INFO @ Tue, 16 Jun 2020 09:34:39: 7000000 INFO @ Tue, 16 Jun 2020 09:34:39: 12000000 INFO @ Tue, 16 Jun 2020 09:34:41: 3000000 INFO @ Tue, 16 Jun 2020 09:34:45: 8000000 INFO @ Tue, 16 Jun 2020 09:34:46: 13000000 INFO @ Tue, 16 Jun 2020 09:34:46: 4000000 INFO @ Tue, 16 Jun 2020 09:34:51: 9000000 INFO @ Tue, 16 Jun 2020 09:34:51: 5000000 INFO @ Tue, 16 Jun 2020 09:34:52: 14000000 INFO @ Tue, 16 Jun 2020 09:34:57: 6000000 INFO @ Tue, 16 Jun 2020 09:34:58: 15000000 INFO @ Tue, 16 Jun 2020 09:34:58: 10000000 INFO @ Tue, 16 Jun 2020 09:35:02: 7000000 INFO @ Tue, 16 Jun 2020 09:35:04: 16000000 INFO @ Tue, 16 Jun 2020 09:35:04: 11000000 INFO @ Tue, 16 Jun 2020 09:35:08: 8000000 INFO @ Tue, 16 Jun 2020 09:35:10: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:35:10: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:35:10: #1 total tags in treatment: 16923928 INFO @ Tue, 16 Jun 2020 09:35:10: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:35:10: #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 09:35:10: #1 tags after filtering in treatment: 16923928 INFO @ Tue, 16 Jun 2020 09:35:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:35:10: #1 finished! INFO @ Tue, 16 Jun 2020 09:35:10: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:35:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:35:10: 12000000 INFO @ Tue, 16 Jun 2020 09:35:11: #2 number of paired peaks: 456 WARNING @ Tue, 16 Jun 2020 09:35:11: Fewer paired peaks (456) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 456 pairs to build model! INFO @ Tue, 16 Jun 2020 09:35:11: start model_add_line... INFO @ Tue, 16 Jun 2020 09:35:11: start X-correlation... INFO @ Tue, 16 Jun 2020 09:35:11: end of X-cor INFO @ Tue, 16 Jun 2020 09:35:11: #2 finished! INFO @ Tue, 16 Jun 2020 09:35:11: #2 predicted fragment length is 79 bps INFO @ Tue, 16 Jun 2020 09:35:11: #2 alternative fragment length(s) may be 2,79 bps INFO @ Tue, 16 Jun 2020 09:35:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020744/SRX5020744.05_model.r WARNING @ Tue, 16 Jun 2020 09:35:11: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:35:11: #2 You may need to consider one of the other alternative d(s): 2,79 WARNING @ Tue, 16 Jun 2020 09:35:11: #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 09:35:11: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:35:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:35:13: 9000000 INFO @ Tue, 16 Jun 2020 09:35:17: 13000000 INFO @ Tue, 16 Jun 2020 09:35:18: 10000000 INFO @ Tue, 16 Jun 2020 09:35:23: 14000000 INFO @ Tue, 16 Jun 2020 09:35:23: 11000000 INFO @ Tue, 16 Jun 2020 09:35:29: 12000000 INFO @ Tue, 16 Jun 2020 09:35:29: 15000000 INFO @ Tue, 16 Jun 2020 09:35:34: 13000000 INFO @ Tue, 16 Jun 2020 09:35:35: 16000000 INFO @ Tue, 16 Jun 2020 09:35:39: 14000000 INFO @ Tue, 16 Jun 2020 09:35:41: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:35:41: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:35:41: #1 total tags in treatment: 16923928 INFO @ Tue, 16 Jun 2020 09:35:41: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:35:41: #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 09:35:42: #1 tags after filtering in treatment: 16923928 INFO @ Tue, 16 Jun 2020 09:35:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:35:42: #1 finished! INFO @ Tue, 16 Jun 2020 09:35:42: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:35:42: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:35:42: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:35:43: #2 number of paired peaks: 456 WARNING @ Tue, 16 Jun 2020 09:35:43: Fewer paired peaks (456) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 456 pairs to build model! INFO @ Tue, 16 Jun 2020 09:35:43: start model_add_line... INFO @ Tue, 16 Jun 2020 09:35:43: start X-correlation... INFO @ Tue, 16 Jun 2020 09:35:43: end of X-cor INFO @ Tue, 16 Jun 2020 09:35:43: #2 finished! INFO @ Tue, 16 Jun 2020 09:35:43: #2 predicted fragment length is 79 bps INFO @ Tue, 16 Jun 2020 09:35:43: #2 alternative fragment length(s) may be 2,79 bps INFO @ Tue, 16 Jun 2020 09:35:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020744/SRX5020744.10_model.r WARNING @ Tue, 16 Jun 2020 09:35:43: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:35:43: #2 You may need to consider one of the other alternative d(s): 2,79 WARNING @ Tue, 16 Jun 2020 09:35:43: #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 09:35:43: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:35:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:35:44: 15000000 INFO @ Tue, 16 Jun 2020 09:35:50: 16000000 INFO @ Tue, 16 Jun 2020 09:35:55: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:35:55: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:35:55: #1 total tags in treatment: 16923928 INFO @ Tue, 16 Jun 2020 09:35:55: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:35:55: #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 09:35:55: #1 tags after filtering in treatment: 16923928 INFO @ Tue, 16 Jun 2020 09:35:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:35:55: #1 finished! INFO @ Tue, 16 Jun 2020 09:35:55: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:35:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:35:56: #2 number of paired peaks: 456 WARNING @ Tue, 16 Jun 2020 09:35:56: Fewer paired peaks (456) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 456 pairs to build model! INFO @ Tue, 16 Jun 2020 09:35:56: start model_add_line... INFO @ Tue, 16 Jun 2020 09:35:56: start X-correlation... INFO @ Tue, 16 Jun 2020 09:35:56: end of X-cor INFO @ Tue, 16 Jun 2020 09:35:56: #2 finished! INFO @ Tue, 16 Jun 2020 09:35:56: #2 predicted fragment length is 79 bps INFO @ Tue, 16 Jun 2020 09:35:56: #2 alternative fragment length(s) may be 2,79 bps INFO @ Tue, 16 Jun 2020 09:35:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020744/SRX5020744.20_model.r WARNING @ Tue, 16 Jun 2020 09:35:56: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:35:56: #2 You may need to consider one of the other alternative d(s): 2,79 WARNING @ Tue, 16 Jun 2020 09:35:56: #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 09:35:56: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:35:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:35:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020744/SRX5020744.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:35:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020744/SRX5020744.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:35:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020744/SRX5020744.05_summits.bed INFO @ Tue, 16 Jun 2020 09:35:58: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1531 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:36:15: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:36:28: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:36:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020744/SRX5020744.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:36:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020744/SRX5020744.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:36:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020744/SRX5020744.10_summits.bed INFO @ Tue, 16 Jun 2020 09:36:30: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (596 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:36:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020744/SRX5020744.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:36:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020744/SRX5020744.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:36:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020744/SRX5020744.20_summits.bed INFO @ Tue, 16 Jun 2020 09:36:44: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (236 records, 4 fields): 1 millis CompletedMACS2peakCalling