Job ID = 6497426 SRX = SRX494838 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T22:16:45 prefetch.2.10.7: 1) Downloading 'SRR1198370'... 2020-06-25T22:16:45 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:20:52 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:20:52 prefetch.2.10.7: 1) 'SRR1198370' was downloaded successfully Read 33596184 spots for SRR1198370/SRR1198370.sra Written 33596184 spots for SRR1198370/SRR1198370.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: 00:00:01 Multiseed full-index search: 00:07:22 33596184 reads; of these: 33596184 (100.00%) were unpaired; of these: 1331622 (3.96%) aligned 0 times 26714997 (79.52%) aligned exactly 1 time 5549565 (16.52%) aligned >1 times 96.04% overall alignment rate Time searching: 00:07:23 Overall time: 00:07:23 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 16 files... [bam_rmdupse_core] 8276070 / 32264562 = 0.2565 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 07:37:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494838/SRX494838.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494838/SRX494838.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494838/SRX494838.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494838/SRX494838.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 07:37:04: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:37:04: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:37:10: 1000000 INFO @ Fri, 26 Jun 2020 07:37:16: 2000000 INFO @ Fri, 26 Jun 2020 07:37:22: 3000000 INFO @ Fri, 26 Jun 2020 07:37:27: 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 @ Fri, 26 Jun 2020 07:37:33: 5000000 INFO @ Fri, 26 Jun 2020 07:37:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494838/SRX494838.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494838/SRX494838.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494838/SRX494838.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494838/SRX494838.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 07:37:34: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:37:34: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:37:39: 6000000 INFO @ Fri, 26 Jun 2020 07:37:42: 1000000 INFO @ Fri, 26 Jun 2020 07:37:46: 7000000 INFO @ Fri, 26 Jun 2020 07:37:50: 2000000 INFO @ Fri, 26 Jun 2020 07:37:53: 8000000 INFO @ Fri, 26 Jun 2020 07:37:58: 3000000 INFO @ Fri, 26 Jun 2020 07:38:00: 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 07:38:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494838/SRX494838.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494838/SRX494838.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494838/SRX494838.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494838/SRX494838.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 07:38:04: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:38:04: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:38:05: 4000000 INFO @ Fri, 26 Jun 2020 07:38:07: 10000000 INFO @ Fri, 26 Jun 2020 07:38:12: 1000000 INFO @ Fri, 26 Jun 2020 07:38:13: 5000000 INFO @ Fri, 26 Jun 2020 07:38:14: 11000000 INFO @ Fri, 26 Jun 2020 07:38:20: 2000000 INFO @ Fri, 26 Jun 2020 07:38:21: 6000000 INFO @ Fri, 26 Jun 2020 07:38:21: 12000000 INFO @ Fri, 26 Jun 2020 07:38:27: 3000000 INFO @ Fri, 26 Jun 2020 07:38:28: 13000000 INFO @ Fri, 26 Jun 2020 07:38:28: 7000000 INFO @ Fri, 26 Jun 2020 07:38:35: 4000000 INFO @ Fri, 26 Jun 2020 07:38:35: 14000000 INFO @ Fri, 26 Jun 2020 07:38:36: 8000000 INFO @ Fri, 26 Jun 2020 07:38:42: 15000000 INFO @ Fri, 26 Jun 2020 07:38:43: 5000000 INFO @ Fri, 26 Jun 2020 07:38:44: 9000000 INFO @ Fri, 26 Jun 2020 07:38:49: 16000000 INFO @ Fri, 26 Jun 2020 07:38:50: 6000000 INFO @ Fri, 26 Jun 2020 07:38:51: 10000000 INFO @ Fri, 26 Jun 2020 07:38:56: 17000000 INFO @ Fri, 26 Jun 2020 07:38:58: 7000000 INFO @ Fri, 26 Jun 2020 07:38:59: 11000000 INFO @ Fri, 26 Jun 2020 07:39:04: 18000000 INFO @ Fri, 26 Jun 2020 07:39:06: 8000000 INFO @ Fri, 26 Jun 2020 07:39:07: 12000000 INFO @ Fri, 26 Jun 2020 07:39:11: 19000000 INFO @ Fri, 26 Jun 2020 07:39:14: 9000000 INFO @ Fri, 26 Jun 2020 07:39:15: 13000000 INFO @ Fri, 26 Jun 2020 07:39:18: 20000000 INFO @ Fri, 26 Jun 2020 07:39:22: 10000000 INFO @ Fri, 26 Jun 2020 07:39:23: 14000000 INFO @ Fri, 26 Jun 2020 07:39:25: 21000000 INFO @ Fri, 26 Jun 2020 07:39:30: 11000000 INFO @ Fri, 26 Jun 2020 07:39:31: 15000000 INFO @ Fri, 26 Jun 2020 07:39:33: 22000000 INFO @ Fri, 26 Jun 2020 07:39:38: 12000000 INFO @ Fri, 26 Jun 2020 07:39:39: 16000000 INFO @ Fri, 26 Jun 2020 07:39:40: 23000000 INFO @ Fri, 26 Jun 2020 07:39:46: 13000000 INFO @ Fri, 26 Jun 2020 07:39:47: 17000000 INFO @ Fri, 26 Jun 2020 07:39:47: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:39:47: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:39:47: #1 total tags in treatment: 23988492 INFO @ Fri, 26 Jun 2020 07:39:47: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:39:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:39:48: #1 tags after filtering in treatment: 23988492 INFO @ Fri, 26 Jun 2020 07:39:48: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:39:48: #1 finished! INFO @ Fri, 26 Jun 2020 07:39:48: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:39:48: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:39:49: #2 number of paired peaks: 182 WARNING @ Fri, 26 Jun 2020 07:39:49: Fewer paired peaks (182) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 182 pairs to build model! INFO @ Fri, 26 Jun 2020 07:39:49: start model_add_line... INFO @ Fri, 26 Jun 2020 07:39:49: start X-correlation... INFO @ Fri, 26 Jun 2020 07:39:49: end of X-cor INFO @ Fri, 26 Jun 2020 07:39:49: #2 finished! INFO @ Fri, 26 Jun 2020 07:39:49: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 07:39:49: #2 alternative fragment length(s) may be 1,14,556,569,588 bps INFO @ Fri, 26 Jun 2020 07:39:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494838/SRX494838.05_model.r WARNING @ Fri, 26 Jun 2020 07:39:49: #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 07:39:49: #2 You may need to consider one of the other alternative d(s): 1,14,556,569,588 WARNING @ Fri, 26 Jun 2020 07:39:49: #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 07:39:49: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:39:49: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:39:54: 14000000 INFO @ Fri, 26 Jun 2020 07:39:55: 18000000 INFO @ Fri, 26 Jun 2020 07:40:01: 15000000 INFO @ Fri, 26 Jun 2020 07:40:03: 19000000 INFO @ Fri, 26 Jun 2020 07:40:09: 16000000 INFO @ Fri, 26 Jun 2020 07:40:10: 20000000 INFO @ Fri, 26 Jun 2020 07:40:17: 17000000 INFO @ Fri, 26 Jun 2020 07:40:18: 21000000 INFO @ Fri, 26 Jun 2020 07:40:25: 18000000 INFO @ Fri, 26 Jun 2020 07:40:26: 22000000 INFO @ Fri, 26 Jun 2020 07:40:27: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:40:33: 19000000 INFO @ Fri, 26 Jun 2020 07:40:34: 23000000 INFO @ Fri, 26 Jun 2020 07:40:41: 20000000 INFO @ Fri, 26 Jun 2020 07:40:42: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:40:42: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:40:42: #1 total tags in treatment: 23988492 INFO @ Fri, 26 Jun 2020 07:40:42: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:40:42: #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 07:40:42: #1 tags after filtering in treatment: 23988492 INFO @ Fri, 26 Jun 2020 07:40:42: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:40:42: #1 finished! INFO @ Fri, 26 Jun 2020 07:40:42: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:40:42: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:40:44: #2 number of paired peaks: 182 WARNING @ Fri, 26 Jun 2020 07:40:44: Fewer paired peaks (182) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 182 pairs to build model! INFO @ Fri, 26 Jun 2020 07:40:44: start model_add_line... INFO @ Fri, 26 Jun 2020 07:40:44: start X-correlation... INFO @ Fri, 26 Jun 2020 07:40:44: end of X-cor INFO @ Fri, 26 Jun 2020 07:40:44: #2 finished! INFO @ Fri, 26 Jun 2020 07:40:44: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 07:40:44: #2 alternative fragment length(s) may be 1,14,556,569,588 bps INFO @ Fri, 26 Jun 2020 07:40:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494838/SRX494838.10_model.r WARNING @ Fri, 26 Jun 2020 07:40:44: #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 07:40:44: #2 You may need to consider one of the other alternative d(s): 1,14,556,569,588 WARNING @ Fri, 26 Jun 2020 07:40:44: #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 07:40:44: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:40:44: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:40:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494838/SRX494838.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:40:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494838/SRX494838.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:40:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494838/SRX494838.05_summits.bed INFO @ Fri, 26 Jun 2020 07:40:45: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:40:49: 21000000 INFO @ Fri, 26 Jun 2020 07:40:56: 22000000 INFO @ Fri, 26 Jun 2020 07:41:04: 23000000 INFO @ Fri, 26 Jun 2020 07:41:11: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:41:11: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:41:11: #1 total tags in treatment: 23988492 INFO @ Fri, 26 Jun 2020 07:41:11: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:41:11: #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 07:41:11: #1 tags after filtering in treatment: 23988492 INFO @ Fri, 26 Jun 2020 07:41:11: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:41:11: #1 finished! INFO @ Fri, 26 Jun 2020 07:41:11: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:41:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:41:13: #2 number of paired peaks: 182 WARNING @ Fri, 26 Jun 2020 07:41:13: Fewer paired peaks (182) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 182 pairs to build model! INFO @ Fri, 26 Jun 2020 07:41:13: start model_add_line... INFO @ Fri, 26 Jun 2020 07:41:13: start X-correlation... INFO @ Fri, 26 Jun 2020 07:41:13: end of X-cor INFO @ Fri, 26 Jun 2020 07:41:13: #2 finished! INFO @ Fri, 26 Jun 2020 07:41:13: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 07:41:13: #2 alternative fragment length(s) may be 1,14,556,569,588 bps INFO @ Fri, 26 Jun 2020 07:41:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494838/SRX494838.20_model.r WARNING @ Fri, 26 Jun 2020 07:41:13: #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 07:41:13: #2 You may need to consider one of the other alternative d(s): 1,14,556,569,588 WARNING @ Fri, 26 Jun 2020 07:41:13: #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 07:41:13: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:41:13: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:41:23: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:41:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494838/SRX494838.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:41:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494838/SRX494838.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:41:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494838/SRX494838.10_summits.bed INFO @ Fri, 26 Jun 2020 07:41:40: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:41:51: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:42:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494838/SRX494838.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:42:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494838/SRX494838.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:42:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494838/SRX494838.20_summits.bed INFO @ Fri, 26 Jun 2020 07:42:08: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling