Job ID = 6367174 SRX = SRX2965748 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:18:01 prefetch.2.10.7: 1) Downloading 'SRR5766333'... 2020-06-15T23:18:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:20:50 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:20:50 prefetch.2.10.7: 1) 'SRR5766333' was downloaded successfully Read 25229792 spots for SRR5766333/SRR5766333.sra Written 25229792 spots for SRR5766333/SRR5766333.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: 00:11:25 25229792 reads; of these: 25229792 (100.00%) were unpaired; of these: 2189560 (8.68%) aligned 0 times 19319147 (76.57%) aligned exactly 1 time 3721085 (14.75%) aligned >1 times 91.32% overall alignment rate Time searching: 00:11:25 Overall time: 00:11:25 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] 2626776 / 23040232 = 0.1140 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 08:41:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2965748/SRX2965748.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2965748/SRX2965748.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2965748/SRX2965748.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2965748/SRX2965748.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 08:41:12: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:41:12: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:41:20: 1000000 INFO @ Tue, 16 Jun 2020 08:41:28: 2000000 INFO @ Tue, 16 Jun 2020 08:41:36: 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 08:41:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2965748/SRX2965748.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2965748/SRX2965748.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2965748/SRX2965748.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2965748/SRX2965748.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 08:41:42: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:41:42: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:41:44: 4000000 INFO @ Tue, 16 Jun 2020 08:41:54: 1000000 INFO @ Tue, 16 Jun 2020 08:41:54: 5000000 INFO @ Tue, 16 Jun 2020 08:42:04: 2000000 INFO @ Tue, 16 Jun 2020 08:42:04: 6000000 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 08:42:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2965748/SRX2965748.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2965748/SRX2965748.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2965748/SRX2965748.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2965748/SRX2965748.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 08:42:12: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:42:12: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:42:15: 7000000 INFO @ Tue, 16 Jun 2020 08:42:15: 3000000 INFO @ Tue, 16 Jun 2020 08:42:24: 1000000 INFO @ Tue, 16 Jun 2020 08:42:25: 8000000 INFO @ Tue, 16 Jun 2020 08:42:27: 4000000 INFO @ Tue, 16 Jun 2020 08:42:35: 2000000 INFO @ Tue, 16 Jun 2020 08:42:36: 9000000 INFO @ Tue, 16 Jun 2020 08:42:38: 5000000 INFO @ Tue, 16 Jun 2020 08:42:46: 10000000 INFO @ Tue, 16 Jun 2020 08:42:46: 3000000 INFO @ Tue, 16 Jun 2020 08:42:49: 6000000 INFO @ Tue, 16 Jun 2020 08:42:57: 11000000 INFO @ Tue, 16 Jun 2020 08:42:58: 4000000 INFO @ Tue, 16 Jun 2020 08:43:00: 7000000 INFO @ Tue, 16 Jun 2020 08:43:07: 12000000 INFO @ Tue, 16 Jun 2020 08:43:09: 5000000 INFO @ Tue, 16 Jun 2020 08:43:12: 8000000 INFO @ Tue, 16 Jun 2020 08:43:17: 13000000 INFO @ Tue, 16 Jun 2020 08:43:20: 6000000 INFO @ Tue, 16 Jun 2020 08:43:23: 9000000 INFO @ Tue, 16 Jun 2020 08:43:27: 14000000 INFO @ Tue, 16 Jun 2020 08:43:31: 7000000 INFO @ Tue, 16 Jun 2020 08:43:34: 10000000 INFO @ Tue, 16 Jun 2020 08:43:38: 15000000 INFO @ Tue, 16 Jun 2020 08:43:43: 8000000 INFO @ Tue, 16 Jun 2020 08:43:45: 11000000 INFO @ Tue, 16 Jun 2020 08:43:48: 16000000 INFO @ Tue, 16 Jun 2020 08:43:54: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:43:56: 12000000 INFO @ Tue, 16 Jun 2020 08:43:58: 17000000 INFO @ Tue, 16 Jun 2020 08:44:05: 10000000 INFO @ Tue, 16 Jun 2020 08:44:07: 13000000 INFO @ Tue, 16 Jun 2020 08:44:08: 18000000 INFO @ Tue, 16 Jun 2020 08:44:16: 11000000 INFO @ Tue, 16 Jun 2020 08:44:18: 14000000 INFO @ Tue, 16 Jun 2020 08:44:18: 19000000 INFO @ Tue, 16 Jun 2020 08:44:27: 12000000 INFO @ Tue, 16 Jun 2020 08:44:28: 20000000 INFO @ Tue, 16 Jun 2020 08:44:29: 15000000 INFO @ Tue, 16 Jun 2020 08:44:33: #1 tag size is determined as 101 bps INFO @ Tue, 16 Jun 2020 08:44:33: #1 tag size = 101 INFO @ Tue, 16 Jun 2020 08:44:33: #1 total tags in treatment: 20413456 INFO @ Tue, 16 Jun 2020 08:44:33: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:44:33: #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 08:44:33: #1 tags after filtering in treatment: 20413456 INFO @ Tue, 16 Jun 2020 08:44:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:44:33: #1 finished! INFO @ Tue, 16 Jun 2020 08:44:33: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:44:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:44:34: #2 number of paired peaks: 140 WARNING @ Tue, 16 Jun 2020 08:44:34: Fewer paired peaks (140) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 140 pairs to build model! INFO @ Tue, 16 Jun 2020 08:44:34: start model_add_line... INFO @ Tue, 16 Jun 2020 08:44:34: start X-correlation... INFO @ Tue, 16 Jun 2020 08:44:34: end of X-cor INFO @ Tue, 16 Jun 2020 08:44:34: #2 finished! INFO @ Tue, 16 Jun 2020 08:44:34: #2 predicted fragment length is 96 bps INFO @ Tue, 16 Jun 2020 08:44:34: #2 alternative fragment length(s) may be 3,96,549 bps INFO @ Tue, 16 Jun 2020 08:44:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2965748/SRX2965748.05_model.r WARNING @ Tue, 16 Jun 2020 08:44:34: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:44:34: #2 You may need to consider one of the other alternative d(s): 3,96,549 WARNING @ Tue, 16 Jun 2020 08:44:34: #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 08:44:34: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:44:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:44:38: 13000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:44:39: 16000000 INFO @ Tue, 16 Jun 2020 08:44:49: 14000000 INFO @ Tue, 16 Jun 2020 08:44:50: 17000000 INFO @ Tue, 16 Jun 2020 08:45:00: 15000000 INFO @ Tue, 16 Jun 2020 08:45:01: 18000000 INFO @ Tue, 16 Jun 2020 08:45:09: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:45:11: 16000000 INFO @ Tue, 16 Jun 2020 08:45:12: 19000000 INFO @ Tue, 16 Jun 2020 08:45:22: 17000000 INFO @ Tue, 16 Jun 2020 08:45:22: 20000000 INFO @ Tue, 16 Jun 2020 08:45:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2965748/SRX2965748.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:45:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2965748/SRX2965748.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:45:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2965748/SRX2965748.05_summits.bed INFO @ Tue, 16 Jun 2020 08:45:25: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (549 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:45:27: #1 tag size is determined as 101 bps INFO @ Tue, 16 Jun 2020 08:45:27: #1 tag size = 101 INFO @ Tue, 16 Jun 2020 08:45:27: #1 total tags in treatment: 20413456 INFO @ Tue, 16 Jun 2020 08:45:27: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:45:27: #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 08:45:27: #1 tags after filtering in treatment: 20413456 INFO @ Tue, 16 Jun 2020 08:45:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:45:27: #1 finished! INFO @ Tue, 16 Jun 2020 08:45:27: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:45:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:45:28: #2 number of paired peaks: 140 WARNING @ Tue, 16 Jun 2020 08:45:28: Fewer paired peaks (140) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 140 pairs to build model! INFO @ Tue, 16 Jun 2020 08:45:28: start model_add_line... INFO @ Tue, 16 Jun 2020 08:45:29: start X-correlation... INFO @ Tue, 16 Jun 2020 08:45:29: end of X-cor INFO @ Tue, 16 Jun 2020 08:45:29: #2 finished! INFO @ Tue, 16 Jun 2020 08:45:29: #2 predicted fragment length is 96 bps INFO @ Tue, 16 Jun 2020 08:45:29: #2 alternative fragment length(s) may be 3,96,549 bps INFO @ Tue, 16 Jun 2020 08:45:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2965748/SRX2965748.10_model.r WARNING @ Tue, 16 Jun 2020 08:45:29: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:45:29: #2 You may need to consider one of the other alternative d(s): 3,96,549 WARNING @ Tue, 16 Jun 2020 08:45:29: #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 08:45:29: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:45:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:45:32: 18000000 INFO @ Tue, 16 Jun 2020 08:45:41: 19000000 INFO @ Tue, 16 Jun 2020 08:45:51: 20000000 INFO @ Tue, 16 Jun 2020 08:45:55: #1 tag size is determined as 101 bps INFO @ Tue, 16 Jun 2020 08:45:55: #1 tag size = 101 INFO @ Tue, 16 Jun 2020 08:45:55: #1 total tags in treatment: 20413456 INFO @ Tue, 16 Jun 2020 08:45:55: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:45:55: #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 08:45:55: #1 tags after filtering in treatment: 20413456 INFO @ Tue, 16 Jun 2020 08:45:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:45:55: #1 finished! INFO @ Tue, 16 Jun 2020 08:45:55: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:45:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:45:57: #2 number of paired peaks: 140 WARNING @ Tue, 16 Jun 2020 08:45:57: Fewer paired peaks (140) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 140 pairs to build model! INFO @ Tue, 16 Jun 2020 08:45:57: start model_add_line... INFO @ Tue, 16 Jun 2020 08:45:57: start X-correlation... INFO @ Tue, 16 Jun 2020 08:45:57: end of X-cor INFO @ Tue, 16 Jun 2020 08:45:57: #2 finished! INFO @ Tue, 16 Jun 2020 08:45:57: #2 predicted fragment length is 96 bps INFO @ Tue, 16 Jun 2020 08:45:57: #2 alternative fragment length(s) may be 3,96,549 bps INFO @ Tue, 16 Jun 2020 08:45:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2965748/SRX2965748.20_model.r WARNING @ Tue, 16 Jun 2020 08:45:57: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:45:57: #2 You may need to consider one of the other alternative d(s): 3,96,549 WARNING @ Tue, 16 Jun 2020 08:45:57: #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 08:45:57: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:45:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:46:01: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:46:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2965748/SRX2965748.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:46:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2965748/SRX2965748.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:46:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2965748/SRX2965748.10_summits.bed INFO @ Tue, 16 Jun 2020 08:46:17: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (421 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:46:29: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:46:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2965748/SRX2965748.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:46:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2965748/SRX2965748.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:46:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2965748/SRX2965748.20_summits.bed INFO @ Tue, 16 Jun 2020 08:46:45: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (236 records, 4 fields): 2 millis CompletedMACS2peakCalling