Job ID = 6368015 SRX = SRX466478 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:48:18 prefetch.2.10.7: 1) Downloading 'SRR1163544'... 2020-06-15T23:48:18 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:51:37 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:51:37 prefetch.2.10.7: 1) 'SRR1163544' was downloaded successfully Read 24825986 spots for SRR1163544/SRR1163544.sra Written 24825986 spots for SRR1163544/SRR1163544.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: 00:06:10 24825986 reads; of these: 24825986 (100.00%) were unpaired; of these: 815606 (3.29%) aligned 0 times 19996341 (80.55%) aligned exactly 1 time 4014039 (16.17%) aligned >1 times 96.71% overall alignment rate Time searching: 00:06:10 Overall time: 00:06:10 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] 6184686 / 24010380 = 0.2576 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 09:05:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466478/SRX466478.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466478/SRX466478.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466478/SRX466478.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466478/SRX466478.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 09:05:19: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:05:19: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:05:25: 1000000 INFO @ Tue, 16 Jun 2020 09:05:30: 2000000 INFO @ Tue, 16 Jun 2020 09:05:36: 3000000 INFO @ Tue, 16 Jun 2020 09:05:41: 4000000 INFO @ Tue, 16 Jun 2020 09:05:47: 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 @ Tue, 16 Jun 2020 09:05:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466478/SRX466478.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466478/SRX466478.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466478/SRX466478.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466478/SRX466478.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 09:05:49: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:05:49: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:05:53: 6000000 INFO @ Tue, 16 Jun 2020 09:05:55: 1000000 INFO @ Tue, 16 Jun 2020 09:05:59: 7000000 INFO @ Tue, 16 Jun 2020 09:06:01: 2000000 INFO @ Tue, 16 Jun 2020 09:06:05: 8000000 INFO @ Tue, 16 Jun 2020 09:06:08: 3000000 INFO @ Tue, 16 Jun 2020 09:06:11: 9000000 INFO @ Tue, 16 Jun 2020 09:06:14: 4000000 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 09:06:18: 10000000 INFO @ Tue, 16 Jun 2020 09:06:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466478/SRX466478.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466478/SRX466478.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466478/SRX466478.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466478/SRX466478.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 09:06:19: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:06:19: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:06:20: 5000000 INFO @ Tue, 16 Jun 2020 09:06:24: 11000000 INFO @ Tue, 16 Jun 2020 09:06:25: 1000000 INFO @ Tue, 16 Jun 2020 09:06:26: 6000000 INFO @ Tue, 16 Jun 2020 09:06:30: 12000000 INFO @ Tue, 16 Jun 2020 09:06:32: 2000000 INFO @ Tue, 16 Jun 2020 09:06:32: 7000000 INFO @ Tue, 16 Jun 2020 09:06:36: 13000000 INFO @ Tue, 16 Jun 2020 09:06:38: 3000000 INFO @ Tue, 16 Jun 2020 09:06:39: 8000000 INFO @ Tue, 16 Jun 2020 09:06:43: 14000000 INFO @ Tue, 16 Jun 2020 09:06:44: 4000000 INFO @ Tue, 16 Jun 2020 09:06:45: 9000000 INFO @ Tue, 16 Jun 2020 09:06:49: 15000000 INFO @ Tue, 16 Jun 2020 09:06:51: 5000000 INFO @ Tue, 16 Jun 2020 09:06:51: 10000000 INFO @ Tue, 16 Jun 2020 09:06:55: 16000000 INFO @ Tue, 16 Jun 2020 09:06:57: 6000000 INFO @ Tue, 16 Jun 2020 09:06:58: 11000000 INFO @ Tue, 16 Jun 2020 09:07:01: 17000000 INFO @ Tue, 16 Jun 2020 09:07:03: 7000000 INFO @ Tue, 16 Jun 2020 09:07:04: 12000000 INFO @ Tue, 16 Jun 2020 09:07:07: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:07:07: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:07:07: #1 total tags in treatment: 17825694 INFO @ Tue, 16 Jun 2020 09:07:07: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:07:07: #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 09:07:07: #1 tags after filtering in treatment: 17825694 INFO @ Tue, 16 Jun 2020 09:07:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:07:07: #1 finished! INFO @ Tue, 16 Jun 2020 09:07:07: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:07:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:07:08: #2 number of paired peaks: 218 WARNING @ Tue, 16 Jun 2020 09:07:08: Fewer paired peaks (218) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 218 pairs to build model! INFO @ Tue, 16 Jun 2020 09:07:08: start model_add_line... INFO @ Tue, 16 Jun 2020 09:07:08: start X-correlation... INFO @ Tue, 16 Jun 2020 09:07:08: end of X-cor INFO @ Tue, 16 Jun 2020 09:07:08: #2 finished! INFO @ Tue, 16 Jun 2020 09:07:08: #2 predicted fragment length is 47 bps INFO @ Tue, 16 Jun 2020 09:07:08: #2 alternative fragment length(s) may be 1,47 bps INFO @ Tue, 16 Jun 2020 09:07:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466478/SRX466478.05_model.r WARNING @ Tue, 16 Jun 2020 09:07:08: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:07:08: #2 You may need to consider one of the other alternative d(s): 1,47 WARNING @ Tue, 16 Jun 2020 09:07:08: #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 09:07:08: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:07:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:07:10: 8000000 INFO @ Tue, 16 Jun 2020 09:07:10: 13000000 INFO @ Tue, 16 Jun 2020 09:07:16: 9000000 INFO @ Tue, 16 Jun 2020 09:07:17: 14000000 INFO @ Tue, 16 Jun 2020 09:07:22: 10000000 INFO @ Tue, 16 Jun 2020 09:07:23: 15000000 INFO @ Tue, 16 Jun 2020 09:07:29: 11000000 INFO @ Tue, 16 Jun 2020 09:07:29: 16000000 INFO @ Tue, 16 Jun 2020 09:07:35: 17000000 INFO @ Tue, 16 Jun 2020 09:07:36: 12000000 INFO @ Tue, 16 Jun 2020 09:07:41: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:07:41: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:07:41: #1 total tags in treatment: 17825694 INFO @ Tue, 16 Jun 2020 09:07:41: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:07:41: #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 09:07:41: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:07:41: #1 tags after filtering in treatment: 17825694 INFO @ Tue, 16 Jun 2020 09:07:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:07:41: #1 finished! INFO @ Tue, 16 Jun 2020 09:07:41: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:07:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:07:42: 13000000 INFO @ Tue, 16 Jun 2020 09:07:42: #2 number of paired peaks: 218 WARNING @ Tue, 16 Jun 2020 09:07:42: Fewer paired peaks (218) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 218 pairs to build model! INFO @ Tue, 16 Jun 2020 09:07:42: start model_add_line... INFO @ Tue, 16 Jun 2020 09:07:42: start X-correlation... INFO @ Tue, 16 Jun 2020 09:07:42: end of X-cor INFO @ Tue, 16 Jun 2020 09:07:42: #2 finished! INFO @ Tue, 16 Jun 2020 09:07:42: #2 predicted fragment length is 47 bps INFO @ Tue, 16 Jun 2020 09:07:42: #2 alternative fragment length(s) may be 1,47 bps INFO @ Tue, 16 Jun 2020 09:07:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466478/SRX466478.10_model.r WARNING @ Tue, 16 Jun 2020 09:07:42: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:07:42: #2 You may need to consider one of the other alternative d(s): 1,47 WARNING @ Tue, 16 Jun 2020 09:07:42: #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 09:07:42: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:07:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:07:48: 14000000 INFO @ Tue, 16 Jun 2020 09:07:54: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:07:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466478/SRX466478.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:07:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466478/SRX466478.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:07:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466478/SRX466478.05_summits.bed INFO @ Tue, 16 Jun 2020 09:07:57: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1018 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:08:00: 16000000 INFO @ Tue, 16 Jun 2020 09:08:06: 17000000 INFO @ Tue, 16 Jun 2020 09:08:11: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:08:11: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:08:11: #1 total tags in treatment: 17825694 INFO @ Tue, 16 Jun 2020 09:08:11: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:08:11: #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 09:08:11: #1 tags after filtering in treatment: 17825694 INFO @ Tue, 16 Jun 2020 09:08:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:08:11: #1 finished! INFO @ Tue, 16 Jun 2020 09:08:11: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:08:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:08:12: #2 number of paired peaks: 218 WARNING @ Tue, 16 Jun 2020 09:08:12: Fewer paired peaks (218) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 218 pairs to build model! INFO @ Tue, 16 Jun 2020 09:08:12: start model_add_line... INFO @ Tue, 16 Jun 2020 09:08:12: start X-correlation... INFO @ Tue, 16 Jun 2020 09:08:12: end of X-cor INFO @ Tue, 16 Jun 2020 09:08:12: #2 finished! INFO @ Tue, 16 Jun 2020 09:08:12: #2 predicted fragment length is 47 bps INFO @ Tue, 16 Jun 2020 09:08:12: #2 alternative fragment length(s) may be 1,47 bps INFO @ Tue, 16 Jun 2020 09:08:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466478/SRX466478.20_model.r WARNING @ Tue, 16 Jun 2020 09:08:12: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:08:12: #2 You may need to consider one of the other alternative d(s): 1,47 WARNING @ Tue, 16 Jun 2020 09:08:12: #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 09:08:12: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:08:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:08:16: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:08:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466478/SRX466478.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:08:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466478/SRX466478.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:08:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466478/SRX466478.10_summits.bed INFO @ Tue, 16 Jun 2020 09:08:33: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (520 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:08:47: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:09:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466478/SRX466478.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:09:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466478/SRX466478.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:09:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466478/SRX466478.20_summits.bed INFO @ Tue, 16 Jun 2020 09:09:04: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (190 records, 4 fields): 1 millis CompletedMACS2peakCalling