Job ID = 6368557 SRX = SRX5020784 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:22:21 prefetch.2.10.7: 1) Downloading 'SRR8201407'... 2020-06-16T00:22:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:24:17 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:24:17 prefetch.2.10.7: 'SRR8201407' is valid 2020-06-16T00:24:17 prefetch.2.10.7: 1) 'SRR8201407' was downloaded successfully 2020-06-16T00:24:17 prefetch.2.10.7: 'SRR8201407' has 0 unresolved dependencies Read 17029652 spots for SRR8201407/SRR8201407.sra Written 17029652 spots for SRR8201407/SRR8201407.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: 00:06:00 17029652 reads; of these: 17029652 (100.00%) were unpaired; of these: 2369126 (13.91%) aligned 0 times 11787576 (69.22%) aligned exactly 1 time 2872950 (16.87%) aligned >1 times 86.09% overall alignment rate Time searching: 00:06:00 Overall time: 00:06:00 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] 2414351 / 14660526 = 0.1647 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 09:35:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020784/SRX5020784.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020784/SRX5020784.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020784/SRX5020784.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020784/SRX5020784.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 09:35:14: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:35:14: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:35:21: 1000000 INFO @ Tue, 16 Jun 2020 09:35:27: 2000000 INFO @ Tue, 16 Jun 2020 09:35:33: 3000000 INFO @ Tue, 16 Jun 2020 09:35:40: 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 09:35:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020784/SRX5020784.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020784/SRX5020784.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020784/SRX5020784.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020784/SRX5020784.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 09:35:44: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:35:44: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:35:46: 5000000 INFO @ Tue, 16 Jun 2020 09:35:52: 1000000 INFO @ Tue, 16 Jun 2020 09:35:54: 6000000 INFO @ Tue, 16 Jun 2020 09:35:59: 2000000 INFO @ Tue, 16 Jun 2020 09:36:01: 7000000 INFO @ Tue, 16 Jun 2020 09:36:07: 3000000 INFO @ Tue, 16 Jun 2020 09:36:09: 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 09:36:14: 4000000 INFO @ Tue, 16 Jun 2020 09:36:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5020784/SRX5020784.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5020784/SRX5020784.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5020784/SRX5020784.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5020784/SRX5020784.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 09:36:14: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:36:14: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:36:16: 9000000 INFO @ Tue, 16 Jun 2020 09:36:22: 5000000 INFO @ Tue, 16 Jun 2020 09:36:23: 1000000 INFO @ Tue, 16 Jun 2020 09:36:24: 10000000 INFO @ Tue, 16 Jun 2020 09:36:29: 6000000 INFO @ Tue, 16 Jun 2020 09:36:31: 2000000 INFO @ Tue, 16 Jun 2020 09:36:31: 11000000 INFO @ Tue, 16 Jun 2020 09:36:37: 7000000 INFO @ Tue, 16 Jun 2020 09:36:39: 12000000 INFO @ Tue, 16 Jun 2020 09:36:39: 3000000 INFO @ Tue, 16 Jun 2020 09:36:40: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:36:40: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:36:40: #1 total tags in treatment: 12246175 INFO @ Tue, 16 Jun 2020 09:36:40: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:36:40: #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 09:36:41: #1 tags after filtering in treatment: 12246175 INFO @ Tue, 16 Jun 2020 09:36:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:36:41: #1 finished! INFO @ Tue, 16 Jun 2020 09:36:41: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:36:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:36:41: #2 number of paired peaks: 452 WARNING @ Tue, 16 Jun 2020 09:36:41: Fewer paired peaks (452) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 452 pairs to build model! INFO @ Tue, 16 Jun 2020 09:36:41: start model_add_line... INFO @ Tue, 16 Jun 2020 09:36:41: start X-correlation... INFO @ Tue, 16 Jun 2020 09:36:42: end of X-cor INFO @ Tue, 16 Jun 2020 09:36:42: #2 finished! INFO @ Tue, 16 Jun 2020 09:36:42: #2 predicted fragment length is 94 bps INFO @ Tue, 16 Jun 2020 09:36:42: #2 alternative fragment length(s) may be 94 bps INFO @ Tue, 16 Jun 2020 09:36:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020784/SRX5020784.05_model.r WARNING @ Tue, 16 Jun 2020 09:36:42: #2 Since the d (94) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:36:42: #2 You may need to consider one of the other alternative d(s): 94 WARNING @ Tue, 16 Jun 2020 09:36:42: #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 09:36:42: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:36:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:36:44: 8000000 INFO @ Tue, 16 Jun 2020 09:36:48: 4000000 INFO @ Tue, 16 Jun 2020 09:36:52: 9000000 INFO @ Tue, 16 Jun 2020 09:36:56: 5000000 INFO @ Tue, 16 Jun 2020 09:36:59: 10000000 INFO @ Tue, 16 Jun 2020 09:37:04: 6000000 INFO @ Tue, 16 Jun 2020 09:37:05: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:37:07: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:37:13: 7000000 INFO @ Tue, 16 Jun 2020 09:37:15: 12000000 INFO @ Tue, 16 Jun 2020 09:37:17: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:37:17: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:37:17: #1 total tags in treatment: 12246175 INFO @ Tue, 16 Jun 2020 09:37:17: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:37:17: #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 09:37:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020784/SRX5020784.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:37:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020784/SRX5020784.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:37:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020784/SRX5020784.05_summits.bed INFO @ Tue, 16 Jun 2020 09:37:17: Done! INFO @ Tue, 16 Jun 2020 09:37:17: #1 tags after filtering in treatment: 12246175 INFO @ Tue, 16 Jun 2020 09:37:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:37:17: #1 finished! INFO @ Tue, 16 Jun 2020 09:37:17: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:37:17: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2255 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:37:18: #2 number of paired peaks: 452 WARNING @ Tue, 16 Jun 2020 09:37:18: Fewer paired peaks (452) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 452 pairs to build model! INFO @ Tue, 16 Jun 2020 09:37:18: start model_add_line... INFO @ Tue, 16 Jun 2020 09:37:18: start X-correlation... INFO @ Tue, 16 Jun 2020 09:37:18: end of X-cor INFO @ Tue, 16 Jun 2020 09:37:18: #2 finished! INFO @ Tue, 16 Jun 2020 09:37:18: #2 predicted fragment length is 94 bps INFO @ Tue, 16 Jun 2020 09:37:18: #2 alternative fragment length(s) may be 94 bps INFO @ Tue, 16 Jun 2020 09:37:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020784/SRX5020784.10_model.r WARNING @ Tue, 16 Jun 2020 09:37:18: #2 Since the d (94) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:37:18: #2 You may need to consider one of the other alternative d(s): 94 WARNING @ Tue, 16 Jun 2020 09:37:18: #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 09:37:18: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:37:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:37:21: 8000000 INFO @ Tue, 16 Jun 2020 09:37:28: 9000000 INFO @ Tue, 16 Jun 2020 09:37:35: 10000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:37:42: 11000000 INFO @ Tue, 16 Jun 2020 09:37:42: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:37:49: 12000000 INFO @ Tue, 16 Jun 2020 09:37:50: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:37:50: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:37:50: #1 total tags in treatment: 12246175 INFO @ Tue, 16 Jun 2020 09:37:50: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:37:50: #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 09:37:51: #1 tags after filtering in treatment: 12246175 INFO @ Tue, 16 Jun 2020 09:37:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:37:51: #1 finished! INFO @ Tue, 16 Jun 2020 09:37:51: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:37:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:37:51: #2 number of paired peaks: 452 WARNING @ Tue, 16 Jun 2020 09:37:51: Fewer paired peaks (452) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 452 pairs to build model! INFO @ Tue, 16 Jun 2020 09:37:51: start model_add_line... INFO @ Tue, 16 Jun 2020 09:37:52: start X-correlation... INFO @ Tue, 16 Jun 2020 09:37:52: end of X-cor INFO @ Tue, 16 Jun 2020 09:37:52: #2 finished! INFO @ Tue, 16 Jun 2020 09:37:52: #2 predicted fragment length is 94 bps INFO @ Tue, 16 Jun 2020 09:37:52: #2 alternative fragment length(s) may be 94 bps INFO @ Tue, 16 Jun 2020 09:37:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5020784/SRX5020784.20_model.r WARNING @ Tue, 16 Jun 2020 09:37:52: #2 Since the d (94) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:37:52: #2 You may need to consider one of the other alternative d(s): 94 WARNING @ Tue, 16 Jun 2020 09:37:52: #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 09:37:52: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:37:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:37:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020784/SRX5020784.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:37:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020784/SRX5020784.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:37:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020784/SRX5020784.10_summits.bed INFO @ Tue, 16 Jun 2020 09:37:54: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1235 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:38:16: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:38:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5020784/SRX5020784.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:38:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5020784/SRX5020784.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:38:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5020784/SRX5020784.20_summits.bed INFO @ Tue, 16 Jun 2020 09:38:28: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (576 records, 4 fields): 1 millis CompletedMACS2peakCalling