Job ID = 6367913 SRX = SRX4194207 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:51:37 prefetch.2.10.7: 1) Downloading 'SRR7291513'... 2020-06-15T23:51:37 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:52:38 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:52:38 prefetch.2.10.7: 'SRR7291513' is valid 2020-06-15T23:52:38 prefetch.2.10.7: 1) 'SRR7291513' was downloaded successfully 2020-06-15T23:52:38 prefetch.2.10.7: 'SRR7291513' has 0 unresolved dependencies Read 5791692 spots for SRR7291513/SRR7291513.sra Written 5791692 spots for SRR7291513/SRR7291513.sra 2020-06-15T23:53:12 prefetch.2.10.7: 1) Downloading 'SRR7291514'... 2020-06-15T23:53:12 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:54:03 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:54:04 prefetch.2.10.7: 'SRR7291514' is valid 2020-06-15T23:54:04 prefetch.2.10.7: 1) 'SRR7291514' was downloaded successfully 2020-06-15T23:54:04 prefetch.2.10.7: 'SRR7291514' has 0 unresolved dependencies Read 5653337 spots for SRR7291514/SRR7291514.sra Written 5653337 spots for SRR7291514/SRR7291514.sra 2020-06-15T23:54:35 prefetch.2.10.7: 1) Downloading 'SRR7291515'... 2020-06-15T23:54:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:55:39 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:55:39 prefetch.2.10.7: 'SRR7291515' is valid 2020-06-15T23:55:39 prefetch.2.10.7: 1) 'SRR7291515' was downloaded successfully 2020-06-15T23:55:39 prefetch.2.10.7: 'SRR7291515' has 0 unresolved dependencies Read 5783078 spots for SRR7291515/SRR7291515.sra Written 5783078 spots for SRR7291515/SRR7291515.sra 2020-06-15T23:56:16 prefetch.2.10.7: 1) Downloading 'SRR7291516'... 2020-06-15T23:56:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:57:06 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:57:07 prefetch.2.10.7: 'SRR7291516' is valid 2020-06-15T23:57:07 prefetch.2.10.7: 1) 'SRR7291516' was downloaded successfully 2020-06-15T23:57:07 prefetch.2.10.7: 'SRR7291516' has 0 unresolved dependencies Read 5595770 spots for SRR7291516/SRR7291516.sra Written 5595770 spots for SRR7291516/SRR7291516.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: 00:08:50 22823877 reads; of these: 22823877 (100.00%) were unpaired; of these: 359008 (1.57%) aligned 0 times 18905968 (82.83%) aligned exactly 1 time 3558901 (15.59%) aligned >1 times 98.43% overall alignment rate Time searching: 00:08:50 Overall time: 00:08:50 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] 3185609 / 22464869 = 0.1418 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 09:13:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4194207/SRX4194207.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4194207/SRX4194207.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4194207/SRX4194207.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4194207/SRX4194207.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 09:13:53: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:13:53: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:14:01: 1000000 INFO @ Tue, 16 Jun 2020 09:14:07: 2000000 INFO @ Tue, 16 Jun 2020 09:14:14: 3000000 INFO @ Tue, 16 Jun 2020 09:14:21: 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 09:14:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4194207/SRX4194207.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4194207/SRX4194207.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4194207/SRX4194207.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4194207/SRX4194207.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 09:14:24: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:14:24: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:14:28: 5000000 INFO @ Tue, 16 Jun 2020 09:14:32: 1000000 INFO @ Tue, 16 Jun 2020 09:14:36: 6000000 INFO @ Tue, 16 Jun 2020 09:14:39: 2000000 INFO @ Tue, 16 Jun 2020 09:14:43: 7000000 INFO @ Tue, 16 Jun 2020 09:14:47: 3000000 INFO @ Tue, 16 Jun 2020 09:14:51: 8000000 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 09:14:54: 4000000 INFO @ Tue, 16 Jun 2020 09:14:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4194207/SRX4194207.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4194207/SRX4194207.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4194207/SRX4194207.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4194207/SRX4194207.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 09:14:54: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:14:54: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:14:59: 9000000 INFO @ Tue, 16 Jun 2020 09:15:02: 5000000 INFO @ Tue, 16 Jun 2020 09:15:02: 1000000 INFO @ Tue, 16 Jun 2020 09:15:07: 10000000 INFO @ Tue, 16 Jun 2020 09:15:09: 6000000 INFO @ Tue, 16 Jun 2020 09:15:10: 2000000 INFO @ Tue, 16 Jun 2020 09:15:14: 11000000 INFO @ Tue, 16 Jun 2020 09:15:17: 7000000 INFO @ Tue, 16 Jun 2020 09:15:18: 3000000 INFO @ Tue, 16 Jun 2020 09:15:22: 12000000 INFO @ Tue, 16 Jun 2020 09:15:25: 8000000 INFO @ Tue, 16 Jun 2020 09:15:26: 4000000 INFO @ Tue, 16 Jun 2020 09:15:30: 13000000 INFO @ Tue, 16 Jun 2020 09:15:32: 9000000 INFO @ Tue, 16 Jun 2020 09:15:34: 5000000 INFO @ Tue, 16 Jun 2020 09:15:37: 14000000 INFO @ Tue, 16 Jun 2020 09:15:40: 10000000 INFO @ Tue, 16 Jun 2020 09:15:42: 6000000 INFO @ Tue, 16 Jun 2020 09:15:45: 15000000 INFO @ Tue, 16 Jun 2020 09:15:47: 11000000 INFO @ Tue, 16 Jun 2020 09:15:50: 7000000 INFO @ Tue, 16 Jun 2020 09:15:53: 16000000 INFO @ Tue, 16 Jun 2020 09:15:55: 12000000 INFO @ Tue, 16 Jun 2020 09:15:57: 8000000 INFO @ Tue, 16 Jun 2020 09:16:01: 17000000 INFO @ Tue, 16 Jun 2020 09:16:02: 13000000 INFO @ Tue, 16 Jun 2020 09:16:05: 9000000 INFO @ Tue, 16 Jun 2020 09:16:09: 18000000 INFO @ Tue, 16 Jun 2020 09:16:10: 14000000 INFO @ Tue, 16 Jun 2020 09:16:13: 10000000 INFO @ Tue, 16 Jun 2020 09:16:17: 19000000 INFO @ Tue, 16 Jun 2020 09:16:17: 15000000 INFO @ Tue, 16 Jun 2020 09:16:19: #1 tag size is determined as 71 bps INFO @ Tue, 16 Jun 2020 09:16:19: #1 tag size = 71 INFO @ Tue, 16 Jun 2020 09:16:19: #1 total tags in treatment: 19279260 INFO @ Tue, 16 Jun 2020 09:16:19: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:16:19: #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 09:16:19: #1 tags after filtering in treatment: 19279260 INFO @ Tue, 16 Jun 2020 09:16:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:16:19: #1 finished! INFO @ Tue, 16 Jun 2020 09:16:19: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:16:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:16:20: #2 number of paired peaks: 200 WARNING @ Tue, 16 Jun 2020 09:16:20: Fewer paired peaks (200) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 200 pairs to build model! INFO @ Tue, 16 Jun 2020 09:16:20: start model_add_line... INFO @ Tue, 16 Jun 2020 09:16:21: start X-correlation... INFO @ Tue, 16 Jun 2020 09:16:21: end of X-cor INFO @ Tue, 16 Jun 2020 09:16:21: #2 finished! INFO @ Tue, 16 Jun 2020 09:16:21: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 09:16:21: #2 alternative fragment length(s) may be 2,49,560,598 bps INFO @ Tue, 16 Jun 2020 09:16:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4194207/SRX4194207.05_model.r WARNING @ Tue, 16 Jun 2020 09:16:21: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:16:21: #2 You may need to consider one of the other alternative d(s): 2,49,560,598 WARNING @ Tue, 16 Jun 2020 09:16:21: #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 09:16:21: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:16:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:16:21: 11000000 INFO @ Tue, 16 Jun 2020 09:16:25: 16000000 INFO @ Tue, 16 Jun 2020 09:16:28: 12000000 INFO @ Tue, 16 Jun 2020 09:16:32: 17000000 INFO @ Tue, 16 Jun 2020 09:16:36: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:16:40: 18000000 INFO @ Tue, 16 Jun 2020 09:16:43: 14000000 INFO @ Tue, 16 Jun 2020 09:16:48: 19000000 INFO @ Tue, 16 Jun 2020 09:16:50: #1 tag size is determined as 71 bps INFO @ Tue, 16 Jun 2020 09:16:50: #1 tag size = 71 INFO @ Tue, 16 Jun 2020 09:16:50: #1 total tags in treatment: 19279260 INFO @ Tue, 16 Jun 2020 09:16:50: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:16:50: #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 09:16:50: #1 tags after filtering in treatment: 19279260 INFO @ Tue, 16 Jun 2020 09:16:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:16:50: #1 finished! INFO @ Tue, 16 Jun 2020 09:16:50: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:16:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:16:51: 15000000 INFO @ Tue, 16 Jun 2020 09:16:51: #2 number of paired peaks: 200 WARNING @ Tue, 16 Jun 2020 09:16:51: Fewer paired peaks (200) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 200 pairs to build model! INFO @ Tue, 16 Jun 2020 09:16:51: start model_add_line... INFO @ Tue, 16 Jun 2020 09:16:52: start X-correlation... INFO @ Tue, 16 Jun 2020 09:16:52: end of X-cor INFO @ Tue, 16 Jun 2020 09:16:52: #2 finished! INFO @ Tue, 16 Jun 2020 09:16:52: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 09:16:52: #2 alternative fragment length(s) may be 2,49,560,598 bps INFO @ Tue, 16 Jun 2020 09:16:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4194207/SRX4194207.10_model.r WARNING @ Tue, 16 Jun 2020 09:16:52: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:16:52: #2 You may need to consider one of the other alternative d(s): 2,49,560,598 WARNING @ Tue, 16 Jun 2020 09:16:52: #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 09:16:52: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:16:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:16:56: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:16:57: 16000000 INFO @ Tue, 16 Jun 2020 09:17:04: 17000000 INFO @ Tue, 16 Jun 2020 09:17:10: 18000000 INFO @ Tue, 16 Jun 2020 09:17:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4194207/SRX4194207.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:17:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4194207/SRX4194207.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:17:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4194207/SRX4194207.05_summits.bed INFO @ Tue, 16 Jun 2020 09:17:12: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (677 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:17:17: 19000000 INFO @ Tue, 16 Jun 2020 09:17:19: #1 tag size is determined as 71 bps INFO @ Tue, 16 Jun 2020 09:17:19: #1 tag size = 71 INFO @ Tue, 16 Jun 2020 09:17:19: #1 total tags in treatment: 19279260 INFO @ Tue, 16 Jun 2020 09:17:19: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:17:19: #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 09:17:19: #1 tags after filtering in treatment: 19279260 INFO @ Tue, 16 Jun 2020 09:17:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:17:19: #1 finished! INFO @ Tue, 16 Jun 2020 09:17:19: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:17:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:17:20: #2 number of paired peaks: 200 WARNING @ Tue, 16 Jun 2020 09:17:20: Fewer paired peaks (200) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 200 pairs to build model! INFO @ Tue, 16 Jun 2020 09:17:20: start model_add_line... INFO @ Tue, 16 Jun 2020 09:17:20: start X-correlation... INFO @ Tue, 16 Jun 2020 09:17:20: end of X-cor INFO @ Tue, 16 Jun 2020 09:17:20: #2 finished! INFO @ Tue, 16 Jun 2020 09:17:20: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 09:17:20: #2 alternative fragment length(s) may be 2,49,560,598 bps INFO @ Tue, 16 Jun 2020 09:17:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4194207/SRX4194207.20_model.r WARNING @ Tue, 16 Jun 2020 09:17:20: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:17:20: #2 You may need to consider one of the other alternative d(s): 2,49,560,598 WARNING @ Tue, 16 Jun 2020 09:17:20: #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 09:17:20: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:17:20: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:17:26: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:17:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4194207/SRX4194207.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:17:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4194207/SRX4194207.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:17:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4194207/SRX4194207.10_summits.bed INFO @ Tue, 16 Jun 2020 09:17:42: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (443 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:17:54: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:18:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4194207/SRX4194207.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:18:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4194207/SRX4194207.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:18:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4194207/SRX4194207.20_summits.bed INFO @ Tue, 16 Jun 2020 09:18:09: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (179 records, 4 fields): 1 millis CompletedMACS2peakCalling