Job ID = 6497441 SRX = SRX494939 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T22:04:19 prefetch.2.10.7: 1) Downloading 'SRR1198471'... 2020-06-25T22:04:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:06:44 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:06:44 prefetch.2.10.7: 1) 'SRR1198471' was downloaded successfully Read 22970231 spots for SRR1198471/SRR1198471.sra Written 22970231 spots for SRR1198471/SRR1198471.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: 00:04:48 22970231 reads; of these: 22970231 (100.00%) were unpaired; of these: 2517600 (10.96%) aligned 0 times 16805583 (73.16%) aligned exactly 1 time 3647048 (15.88%) aligned >1 times 89.04% overall alignment rate Time searching: 00:04:48 Overall time: 00:04:48 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] 2297188 / 20452631 = 0.1123 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 07:17:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494939/SRX494939.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494939/SRX494939.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494939/SRX494939.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494939/SRX494939.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 07:17:57: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:17:57: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:18:02: 1000000 INFO @ Fri, 26 Jun 2020 07:18:07: 2000000 INFO @ Fri, 26 Jun 2020 07:18:12: 3000000 INFO @ Fri, 26 Jun 2020 07:18:17: 4000000 INFO @ Fri, 26 Jun 2020 07:18:22: 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 07:18:27: 6000000 INFO @ Fri, 26 Jun 2020 07:18:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494939/SRX494939.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494939/SRX494939.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494939/SRX494939.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494939/SRX494939.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 07:18:27: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:18:27: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:18:32: 7000000 INFO @ Fri, 26 Jun 2020 07:18:32: 1000000 INFO @ Fri, 26 Jun 2020 07:18:37: 8000000 INFO @ Fri, 26 Jun 2020 07:18:37: 2000000 INFO @ Fri, 26 Jun 2020 07:18:42: 9000000 INFO @ Fri, 26 Jun 2020 07:18:43: 3000000 INFO @ Fri, 26 Jun 2020 07:18:47: 10000000 INFO @ Fri, 26 Jun 2020 07:18:48: 4000000 INFO @ Fri, 26 Jun 2020 07:18:52: 11000000 INFO @ Fri, 26 Jun 2020 07:18:53: 5000000 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 07:18:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494939/SRX494939.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494939/SRX494939.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494939/SRX494939.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494939/SRX494939.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 07:18:57: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:18:57: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:18:57: 12000000 INFO @ Fri, 26 Jun 2020 07:18:58: 6000000 INFO @ Fri, 26 Jun 2020 07:19:02: 1000000 INFO @ Fri, 26 Jun 2020 07:19:02: 13000000 INFO @ Fri, 26 Jun 2020 07:19:04: 7000000 INFO @ Fri, 26 Jun 2020 07:19:08: 14000000 INFO @ Fri, 26 Jun 2020 07:19:08: 2000000 INFO @ Fri, 26 Jun 2020 07:19:09: 8000000 INFO @ Fri, 26 Jun 2020 07:19:13: 15000000 INFO @ Fri, 26 Jun 2020 07:19:13: 3000000 INFO @ Fri, 26 Jun 2020 07:19:14: 9000000 INFO @ Fri, 26 Jun 2020 07:19:18: 16000000 INFO @ Fri, 26 Jun 2020 07:19:18: 4000000 INFO @ Fri, 26 Jun 2020 07:19:19: 10000000 INFO @ Fri, 26 Jun 2020 07:19:23: 17000000 INFO @ Fri, 26 Jun 2020 07:19:23: 5000000 INFO @ Fri, 26 Jun 2020 07:19:25: 11000000 INFO @ Fri, 26 Jun 2020 07:19:28: 18000000 INFO @ Fri, 26 Jun 2020 07:19:29: 6000000 INFO @ Fri, 26 Jun 2020 07:19:29: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:19:29: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:19:29: #1 total tags in treatment: 18155443 INFO @ Fri, 26 Jun 2020 07:19:29: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:19:29: #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 07:19:30: #1 tags after filtering in treatment: 18155443 INFO @ Fri, 26 Jun 2020 07:19:30: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:19:30: #1 finished! INFO @ Fri, 26 Jun 2020 07:19:30: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:19:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:19:30: 12000000 INFO @ Fri, 26 Jun 2020 07:19:31: #2 number of paired peaks: 258 WARNING @ Fri, 26 Jun 2020 07:19:31: Fewer paired peaks (258) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 258 pairs to build model! INFO @ Fri, 26 Jun 2020 07:19:31: start model_add_line... INFO @ Fri, 26 Jun 2020 07:19:31: start X-correlation... INFO @ Fri, 26 Jun 2020 07:19:31: end of X-cor INFO @ Fri, 26 Jun 2020 07:19:31: #2 finished! INFO @ Fri, 26 Jun 2020 07:19:31: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 07:19:31: #2 alternative fragment length(s) may be 1,46,536,574 bps INFO @ Fri, 26 Jun 2020 07:19:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494939/SRX494939.05_model.r WARNING @ Fri, 26 Jun 2020 07:19:31: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:19:31: #2 You may need to consider one of the other alternative d(s): 1,46,536,574 WARNING @ Fri, 26 Jun 2020 07:19:31: #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 07:19:31: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:19:31: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:19:34: 7000000 INFO @ Fri, 26 Jun 2020 07:19:35: 13000000 INFO @ Fri, 26 Jun 2020 07:19:39: 8000000 INFO @ Fri, 26 Jun 2020 07:19:41: 14000000 INFO @ Fri, 26 Jun 2020 07:19:44: 9000000 INFO @ Fri, 26 Jun 2020 07:19:46: 15000000 INFO @ Fri, 26 Jun 2020 07:19:50: 10000000 INFO @ Fri, 26 Jun 2020 07:19:51: 16000000 INFO @ Fri, 26 Jun 2020 07:19:55: 11000000 INFO @ Fri, 26 Jun 2020 07:19:56: 17000000 INFO @ Fri, 26 Jun 2020 07:20:00: 12000000 INFO @ Fri, 26 Jun 2020 07:20:02: 18000000 INFO @ Fri, 26 Jun 2020 07:20:02: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:20:03: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:20:03: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:20:03: #1 total tags in treatment: 18155443 INFO @ Fri, 26 Jun 2020 07:20:03: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:20:03: #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 07:20:03: #1 tags after filtering in treatment: 18155443 INFO @ Fri, 26 Jun 2020 07:20:03: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:20:03: #1 finished! INFO @ Fri, 26 Jun 2020 07:20:03: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:20:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:20:04: #2 number of paired peaks: 258 WARNING @ Fri, 26 Jun 2020 07:20:04: Fewer paired peaks (258) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 258 pairs to build model! INFO @ Fri, 26 Jun 2020 07:20:04: start model_add_line... INFO @ Fri, 26 Jun 2020 07:20:04: start X-correlation... INFO @ Fri, 26 Jun 2020 07:20:04: end of X-cor INFO @ Fri, 26 Jun 2020 07:20:04: #2 finished! INFO @ Fri, 26 Jun 2020 07:20:04: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 07:20:04: #2 alternative fragment length(s) may be 1,46,536,574 bps INFO @ Fri, 26 Jun 2020 07:20:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494939/SRX494939.10_model.r WARNING @ Fri, 26 Jun 2020 07:20:04: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:20:04: #2 You may need to consider one of the other alternative d(s): 1,46,536,574 WARNING @ Fri, 26 Jun 2020 07:20:04: #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 07:20:04: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:20:04: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:20:05: 13000000 INFO @ Fri, 26 Jun 2020 07:20:11: 14000000 INFO @ Fri, 26 Jun 2020 07:20:16: 15000000 INFO @ Fri, 26 Jun 2020 07:20:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494939/SRX494939.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:20:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494939/SRX494939.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:20:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494939/SRX494939.05_summits.bed INFO @ Fri, 26 Jun 2020 07:20:16: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:20:21: 16000000 INFO @ Fri, 26 Jun 2020 07:20:26: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:20:31: 18000000 INFO @ Fri, 26 Jun 2020 07:20:32: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:20:32: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:20:32: #1 total tags in treatment: 18155443 INFO @ Fri, 26 Jun 2020 07:20:32: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:20:32: #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 07:20:33: #1 tags after filtering in treatment: 18155443 INFO @ Fri, 26 Jun 2020 07:20:33: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:20:33: #1 finished! INFO @ Fri, 26 Jun 2020 07:20:33: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:20:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:20:34: #2 number of paired peaks: 258 WARNING @ Fri, 26 Jun 2020 07:20:34: Fewer paired peaks (258) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 258 pairs to build model! INFO @ Fri, 26 Jun 2020 07:20:34: start model_add_line... INFO @ Fri, 26 Jun 2020 07:20:34: start X-correlation... INFO @ Fri, 26 Jun 2020 07:20:34: end of X-cor INFO @ Fri, 26 Jun 2020 07:20:34: #2 finished! INFO @ Fri, 26 Jun 2020 07:20:34: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 07:20:34: #2 alternative fragment length(s) may be 1,46,536,574 bps INFO @ Fri, 26 Jun 2020 07:20:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494939/SRX494939.20_model.r WARNING @ Fri, 26 Jun 2020 07:20:34: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:20:34: #2 You may need to consider one of the other alternative d(s): 1,46,536,574 WARNING @ Fri, 26 Jun 2020 07:20:34: #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 07:20:34: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:20:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:20:35: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:20:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494939/SRX494939.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:20:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494939/SRX494939.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:20:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494939/SRX494939.10_summits.bed INFO @ Fri, 26 Jun 2020 07:20:49: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:21:06: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:21:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494939/SRX494939.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:21:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494939/SRX494939.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:21:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494939/SRX494939.20_summits.bed INFO @ Fri, 26 Jun 2020 07:21:21: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling