Job ID = 6507955 SRX = SRX495115 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T14:02:26 prefetch.2.10.7: 1) Downloading 'SRR1198647'... 2020-06-26T14:02:26 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T14:05:07 prefetch.2.10.7: HTTPS download succeed 2020-06-26T14:05:07 prefetch.2.10.7: 1) 'SRR1198647' was downloaded successfully Read 30872377 spots for SRR1198647/SRR1198647.sra Written 30872377 spots for SRR1198647/SRR1198647.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: 00:05:47 30872377 reads; of these: 30872377 (100.00%) were unpaired; of these: 5276819 (17.09%) aligned 0 times 21034882 (68.13%) aligned exactly 1 time 4560676 (14.77%) aligned >1 times 82.91% overall alignment rate Time searching: 00:05:47 Overall time: 00:05:47 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] 12232772 / 25595558 = 0.4779 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 @ Fri, 26 Jun 2020 23:17:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495115/SRX495115.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495115/SRX495115.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495115/SRX495115.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495115/SRX495115.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 @ Fri, 26 Jun 2020 23:17:09: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:17:09: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:17:15: 1000000 INFO @ Fri, 26 Jun 2020 23:17:20: 2000000 INFO @ Fri, 26 Jun 2020 23:17:26: 3000000 INFO @ Fri, 26 Jun 2020 23:17:31: 4000000 INFO @ Fri, 26 Jun 2020 23:17:37: 5000000 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 @ Fri, 26 Jun 2020 23:17:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495115/SRX495115.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495115/SRX495115.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495115/SRX495115.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495115/SRX495115.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 @ Fri, 26 Jun 2020 23:17:39: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:17:39: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:17:44: 6000000 INFO @ Fri, 26 Jun 2020 23:17:47: 1000000 INFO @ Fri, 26 Jun 2020 23:17:51: 7000000 INFO @ Fri, 26 Jun 2020 23:17:56: 2000000 INFO @ Fri, 26 Jun 2020 23:17:58: 8000000 INFO @ Fri, 26 Jun 2020 23:18:04: 3000000 INFO @ Fri, 26 Jun 2020 23:18:05: 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 @ Fri, 26 Jun 2020 23:18:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495115/SRX495115.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495115/SRX495115.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495115/SRX495115.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495115/SRX495115.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 @ Fri, 26 Jun 2020 23:18:09: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:18:09: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:18:12: 10000000 INFO @ Fri, 26 Jun 2020 23:18:13: 4000000 INFO @ Fri, 26 Jun 2020 23:18:16: 1000000 INFO @ Fri, 26 Jun 2020 23:18:20: 11000000 INFO @ Fri, 26 Jun 2020 23:18:21: 5000000 INFO @ Fri, 26 Jun 2020 23:18:23: 2000000 INFO @ Fri, 26 Jun 2020 23:18:27: 12000000 INFO @ Fri, 26 Jun 2020 23:18:29: 6000000 INFO @ Fri, 26 Jun 2020 23:18:31: 3000000 INFO @ Fri, 26 Jun 2020 23:18:34: 13000000 INFO @ Fri, 26 Jun 2020 23:18:37: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:18:37: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:18:37: #1 total tags in treatment: 13362786 INFO @ Fri, 26 Jun 2020 23:18:37: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:18:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:18:37: #1 tags after filtering in treatment: 13362786 INFO @ Fri, 26 Jun 2020 23:18:37: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:18:37: #1 finished! INFO @ Fri, 26 Jun 2020 23:18:37: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:18:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:18:37: 7000000 INFO @ Fri, 26 Jun 2020 23:18:38: #2 number of paired peaks: 312 WARNING @ Fri, 26 Jun 2020 23:18:38: Fewer paired peaks (312) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 312 pairs to build model! INFO @ Fri, 26 Jun 2020 23:18:38: start model_add_line... INFO @ Fri, 26 Jun 2020 23:18:38: start X-correlation... INFO @ Fri, 26 Jun 2020 23:18:38: end of X-cor INFO @ Fri, 26 Jun 2020 23:18:38: #2 finished! INFO @ Fri, 26 Jun 2020 23:18:38: #2 predicted fragment length is 53 bps INFO @ Fri, 26 Jun 2020 23:18:38: #2 alternative fragment length(s) may be 3,53 bps INFO @ Fri, 26 Jun 2020 23:18:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495115/SRX495115.05_model.r WARNING @ Fri, 26 Jun 2020 23:18:38: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:18:38: #2 You may need to consider one of the other alternative d(s): 3,53 WARNING @ Fri, 26 Jun 2020 23:18:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 23:18:38: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:18:38: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:18:38: 4000000 INFO @ Fri, 26 Jun 2020 23:18:45: 5000000 INFO @ Fri, 26 Jun 2020 23:18:46: 8000000 INFO @ Fri, 26 Jun 2020 23:18:53: 6000000 INFO @ Fri, 26 Jun 2020 23:18:54: 9000000 INFO @ Fri, 26 Jun 2020 23:19:00: 7000000 INFO @ Fri, 26 Jun 2020 23:19:01: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:19:02: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 23:19:07: 8000000 INFO @ Fri, 26 Jun 2020 23:19:10: 11000000 INFO @ Fri, 26 Jun 2020 23:19:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495115/SRX495115.05_peaks.xls INFO @ Fri, 26 Jun 2020 23:19:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495115/SRX495115.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:19:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495115/SRX495115.05_summits.bed INFO @ Fri, 26 Jun 2020 23:19:13: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1780 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:19:15: 9000000 INFO @ Fri, 26 Jun 2020 23:19:19: 12000000 INFO @ Fri, 26 Jun 2020 23:19:22: 10000000 INFO @ Fri, 26 Jun 2020 23:19:26: 13000000 INFO @ Fri, 26 Jun 2020 23:19:29: 11000000 INFO @ Fri, 26 Jun 2020 23:19:29: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:19:29: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:19:29: #1 total tags in treatment: 13362786 INFO @ Fri, 26 Jun 2020 23:19:29: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:19:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:19:29: #1 tags after filtering in treatment: 13362786 INFO @ Fri, 26 Jun 2020 23:19:29: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:19:29: #1 finished! INFO @ Fri, 26 Jun 2020 23:19:29: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:19:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:19:30: #2 number of paired peaks: 312 WARNING @ Fri, 26 Jun 2020 23:19:30: Fewer paired peaks (312) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 312 pairs to build model! INFO @ Fri, 26 Jun 2020 23:19:30: start model_add_line... INFO @ Fri, 26 Jun 2020 23:19:30: start X-correlation... INFO @ Fri, 26 Jun 2020 23:19:30: end of X-cor INFO @ Fri, 26 Jun 2020 23:19:30: #2 finished! INFO @ Fri, 26 Jun 2020 23:19:30: #2 predicted fragment length is 53 bps INFO @ Fri, 26 Jun 2020 23:19:30: #2 alternative fragment length(s) may be 3,53 bps INFO @ Fri, 26 Jun 2020 23:19:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495115/SRX495115.10_model.r WARNING @ Fri, 26 Jun 2020 23:19:30: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:19:30: #2 You may need to consider one of the other alternative d(s): 3,53 WARNING @ Fri, 26 Jun 2020 23:19:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 23:19:30: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:19:30: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 23:19:36: 12000000 INFO @ Fri, 26 Jun 2020 23:19:42: 13000000 INFO @ Fri, 26 Jun 2020 23:19:44: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:19:44: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:19:44: #1 total tags in treatment: 13362786 INFO @ Fri, 26 Jun 2020 23:19:44: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:19:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:19:44: #1 tags after filtering in treatment: 13362786 INFO @ Fri, 26 Jun 2020 23:19:44: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:19:44: #1 finished! INFO @ Fri, 26 Jun 2020 23:19:44: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:19:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:19:45: #2 number of paired peaks: 312 WARNING @ Fri, 26 Jun 2020 23:19:45: Fewer paired peaks (312) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 312 pairs to build model! INFO @ Fri, 26 Jun 2020 23:19:45: start model_add_line... INFO @ Fri, 26 Jun 2020 23:19:45: start X-correlation... INFO @ Fri, 26 Jun 2020 23:19:45: end of X-cor INFO @ Fri, 26 Jun 2020 23:19:45: #2 finished! INFO @ Fri, 26 Jun 2020 23:19:45: #2 predicted fragment length is 53 bps INFO @ Fri, 26 Jun 2020 23:19:45: #2 alternative fragment length(s) may be 3,53 bps INFO @ Fri, 26 Jun 2020 23:19:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495115/SRX495115.20_model.r WARNING @ Fri, 26 Jun 2020 23:19:45: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:19:45: #2 You may need to consider one of the other alternative d(s): 3,53 WARNING @ Fri, 26 Jun 2020 23:19:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 23:19:45: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:19:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:19:55: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:20:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495115/SRX495115.10_peaks.xls INFO @ Fri, 26 Jun 2020 23:20:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495115/SRX495115.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:20:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495115/SRX495115.10_summits.bed INFO @ Fri, 26 Jun 2020 23:20:07: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (548 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:20:10: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:20:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495115/SRX495115.20_peaks.xls INFO @ Fri, 26 Jun 2020 23:20:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495115/SRX495115.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:20:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495115/SRX495115.20_summits.bed INFO @ Fri, 26 Jun 2020 23:20:22: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (187 records, 4 fields): 1 millis CompletedMACS2peakCalling