Job ID = 6366867 SRX = SRX2370185 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:54:44 prefetch.2.10.7: 1) Downloading 'SRR5047586'... 2020-06-15T22:54:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:57:38 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:57:38 prefetch.2.10.7: 1) 'SRR5047586' was downloaded successfully Read 20236840 spots for SRR5047586/SRR5047586.sra Written 20236840 spots for SRR5047586/SRR5047586.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: 00:09:22 20236840 reads; of these: 20236840 (100.00%) were unpaired; of these: 654805 (3.24%) aligned 0 times 16269758 (80.40%) aligned exactly 1 time 3312277 (16.37%) aligned >1 times 96.76% overall alignment rate Time searching: 00:09:22 Overall time: 00:09:22 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] 5733308 / 19582035 = 0.2928 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 08:14:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2370185/SRX2370185.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2370185/SRX2370185.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2370185/SRX2370185.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2370185/SRX2370185.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 08:14:46: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:14:46: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:14:53: 1000000 INFO @ Tue, 16 Jun 2020 08:15:00: 2000000 INFO @ Tue, 16 Jun 2020 08:15:06: 3000000 INFO @ Tue, 16 Jun 2020 08:15:13: 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 08:15:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2370185/SRX2370185.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2370185/SRX2370185.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2370185/SRX2370185.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2370185/SRX2370185.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 08:15:16: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:15:16: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:15:21: 5000000 INFO @ Tue, 16 Jun 2020 08:15:25: 1000000 INFO @ Tue, 16 Jun 2020 08:15:30: 6000000 INFO @ Tue, 16 Jun 2020 08:15:34: 2000000 INFO @ Tue, 16 Jun 2020 08:15:38: 7000000 INFO @ Tue, 16 Jun 2020 08:15:43: 3000000 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 08:15:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2370185/SRX2370185.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2370185/SRX2370185.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2370185/SRX2370185.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2370185/SRX2370185.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 08:15:46: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:15:46: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:15:46: 8000000 INFO @ Tue, 16 Jun 2020 08:15:52: 4000000 INFO @ Tue, 16 Jun 2020 08:15:55: 9000000 INFO @ Tue, 16 Jun 2020 08:15:55: 1000000 INFO @ Tue, 16 Jun 2020 08:16:01: 5000000 INFO @ Tue, 16 Jun 2020 08:16:03: 10000000 INFO @ Tue, 16 Jun 2020 08:16:05: 2000000 INFO @ Tue, 16 Jun 2020 08:16:10: 6000000 INFO @ Tue, 16 Jun 2020 08:16:12: 11000000 INFO @ Tue, 16 Jun 2020 08:16:14: 3000000 INFO @ Tue, 16 Jun 2020 08:16:19: 7000000 INFO @ Tue, 16 Jun 2020 08:16:20: 12000000 INFO @ Tue, 16 Jun 2020 08:16:24: 4000000 INFO @ Tue, 16 Jun 2020 08:16:29: 8000000 INFO @ Tue, 16 Jun 2020 08:16:29: 13000000 INFO @ Tue, 16 Jun 2020 08:16:34: 5000000 INFO @ Tue, 16 Jun 2020 08:16:36: #1 tag size is determined as 100 bps INFO @ Tue, 16 Jun 2020 08:16:36: #1 tag size = 100 INFO @ Tue, 16 Jun 2020 08:16:36: #1 total tags in treatment: 13848727 INFO @ Tue, 16 Jun 2020 08:16:36: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:16:36: #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 08:16:36: #1 tags after filtering in treatment: 13848727 INFO @ Tue, 16 Jun 2020 08:16:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:16:36: #1 finished! INFO @ Tue, 16 Jun 2020 08:16:36: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:16:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:16:37: #2 number of paired peaks: 293 WARNING @ Tue, 16 Jun 2020 08:16:37: Fewer paired peaks (293) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 293 pairs to build model! INFO @ Tue, 16 Jun 2020 08:16:37: start model_add_line... INFO @ Tue, 16 Jun 2020 08:16:37: start X-correlation... INFO @ Tue, 16 Jun 2020 08:16:37: end of X-cor INFO @ Tue, 16 Jun 2020 08:16:37: #2 finished! INFO @ Tue, 16 Jun 2020 08:16:37: #2 predicted fragment length is 94 bps INFO @ Tue, 16 Jun 2020 08:16:37: #2 alternative fragment length(s) may be 3,94 bps INFO @ Tue, 16 Jun 2020 08:16:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2370185/SRX2370185.05_model.r WARNING @ Tue, 16 Jun 2020 08:16:37: #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 08:16:37: #2 You may need to consider one of the other alternative d(s): 3,94 WARNING @ Tue, 16 Jun 2020 08:16:37: #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 08:16:37: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:16:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:16:37: 9000000 INFO @ Tue, 16 Jun 2020 08:16:43: 6000000 INFO @ Tue, 16 Jun 2020 08:16:46: 10000000 INFO @ Tue, 16 Jun 2020 08:16:53: 7000000 INFO @ Tue, 16 Jun 2020 08:16:55: 11000000 INFO @ Tue, 16 Jun 2020 08:17:02: 8000000 INFO @ Tue, 16 Jun 2020 08:17:02: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:17:04: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:17:11: 9000000 INFO @ Tue, 16 Jun 2020 08:17:13: 13000000 INFO @ Tue, 16 Jun 2020 08:17:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2370185/SRX2370185.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:17:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2370185/SRX2370185.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:17:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2370185/SRX2370185.05_summits.bed INFO @ Tue, 16 Jun 2020 08:17:15: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (512 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:17:21: #1 tag size is determined as 100 bps INFO @ Tue, 16 Jun 2020 08:17:21: #1 tag size = 100 INFO @ Tue, 16 Jun 2020 08:17:21: #1 total tags in treatment: 13848727 INFO @ Tue, 16 Jun 2020 08:17:21: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:17:21: #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 08:17:21: 10000000 INFO @ Tue, 16 Jun 2020 08:17:21: #1 tags after filtering in treatment: 13848727 INFO @ Tue, 16 Jun 2020 08:17:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:17:21: #1 finished! INFO @ Tue, 16 Jun 2020 08:17:21: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:17:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:17:22: #2 number of paired peaks: 293 WARNING @ Tue, 16 Jun 2020 08:17:22: Fewer paired peaks (293) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 293 pairs to build model! INFO @ Tue, 16 Jun 2020 08:17:22: start model_add_line... INFO @ Tue, 16 Jun 2020 08:17:22: start X-correlation... INFO @ Tue, 16 Jun 2020 08:17:22: end of X-cor INFO @ Tue, 16 Jun 2020 08:17:22: #2 finished! INFO @ Tue, 16 Jun 2020 08:17:22: #2 predicted fragment length is 94 bps INFO @ Tue, 16 Jun 2020 08:17:22: #2 alternative fragment length(s) may be 3,94 bps INFO @ Tue, 16 Jun 2020 08:17:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2370185/SRX2370185.10_model.r WARNING @ Tue, 16 Jun 2020 08:17:22: #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 08:17:22: #2 You may need to consider one of the other alternative d(s): 3,94 WARNING @ Tue, 16 Jun 2020 08:17:22: #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 08:17:22: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:17:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:17:30: 11000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:17:39: 12000000 INFO @ Tue, 16 Jun 2020 08:17:48: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:17:49: 13000000 INFO @ Tue, 16 Jun 2020 08:17:56: #1 tag size is determined as 100 bps INFO @ Tue, 16 Jun 2020 08:17:56: #1 tag size = 100 INFO @ Tue, 16 Jun 2020 08:17:56: #1 total tags in treatment: 13848727 INFO @ Tue, 16 Jun 2020 08:17:56: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:17:56: #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 08:17:56: #1 tags after filtering in treatment: 13848727 INFO @ Tue, 16 Jun 2020 08:17:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:17:56: #1 finished! INFO @ Tue, 16 Jun 2020 08:17:56: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:17:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:17:57: #2 number of paired peaks: 293 WARNING @ Tue, 16 Jun 2020 08:17:57: Fewer paired peaks (293) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 293 pairs to build model! INFO @ Tue, 16 Jun 2020 08:17:57: start model_add_line... INFO @ Tue, 16 Jun 2020 08:17:57: start X-correlation... INFO @ Tue, 16 Jun 2020 08:17:57: end of X-cor INFO @ Tue, 16 Jun 2020 08:17:57: #2 finished! INFO @ Tue, 16 Jun 2020 08:17:57: #2 predicted fragment length is 94 bps INFO @ Tue, 16 Jun 2020 08:17:57: #2 alternative fragment length(s) may be 3,94 bps INFO @ Tue, 16 Jun 2020 08:17:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2370185/SRX2370185.20_model.r WARNING @ Tue, 16 Jun 2020 08:17:57: #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 08:17:57: #2 You may need to consider one of the other alternative d(s): 3,94 WARNING @ Tue, 16 Jun 2020 08:17:57: #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 08:17:57: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:17:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:18:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2370185/SRX2370185.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:18:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2370185/SRX2370185.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:18:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2370185/SRX2370185.10_summits.bed INFO @ Tue, 16 Jun 2020 08:18:00: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (388 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:18:24: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:18:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2370185/SRX2370185.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:18:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2370185/SRX2370185.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:18:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2370185/SRX2370185.20_summits.bed INFO @ Tue, 16 Jun 2020 08:18:37: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (239 records, 4 fields): 1 millis CompletedMACS2peakCalling