Job ID = 6366050 SRX = SRX059222 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:46:37 prefetch.2.10.7: 1) Downloading 'SRR190662'... 2020-06-15T22:46:37 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:48:59 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:48:59 prefetch.2.10.7: 1) 'SRR190662' was downloaded successfully Read 46755661 spots for SRR190662/SRR190662.sra Written 46755661 spots for SRR190662/SRR190662.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: 00:06:40 46755661 reads; of these: 46755661 (100.00%) were unpaired; of these: 14942997 (31.96%) aligned 0 times 26133642 (55.89%) aligned exactly 1 time 5679022 (12.15%) aligned >1 times 68.04% overall alignment rate Time searching: 00:06:40 Overall time: 00:06:40 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] 4505992 / 31812664 = 0.1416 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 08:04:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059222/SRX059222.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059222/SRX059222.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059222/SRX059222.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059222/SRX059222.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 08:04:49: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:04:49: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:04:55: 1000000 INFO @ Tue, 16 Jun 2020 08:05:01: 2000000 INFO @ Tue, 16 Jun 2020 08:05:07: 3000000 INFO @ Tue, 16 Jun 2020 08:05:14: 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 08:05:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059222/SRX059222.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059222/SRX059222.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059222/SRX059222.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059222/SRX059222.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 08:05:19: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:05:19: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:05:20: 5000000 INFO @ Tue, 16 Jun 2020 08:05:25: 1000000 INFO @ Tue, 16 Jun 2020 08:05:26: 6000000 INFO @ Tue, 16 Jun 2020 08:05:31: 2000000 INFO @ Tue, 16 Jun 2020 08:05:32: 7000000 INFO @ Tue, 16 Jun 2020 08:05:37: 3000000 INFO @ Tue, 16 Jun 2020 08:05:38: 8000000 INFO @ Tue, 16 Jun 2020 08:05:43: 4000000 INFO @ Tue, 16 Jun 2020 08:05:44: 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 @ Tue, 16 Jun 2020 08:05:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059222/SRX059222.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059222/SRX059222.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059222/SRX059222.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059222/SRX059222.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 08:05:49: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:05:49: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:05:49: 5000000 INFO @ Tue, 16 Jun 2020 08:05:50: 10000000 INFO @ Tue, 16 Jun 2020 08:05:55: 1000000 INFO @ Tue, 16 Jun 2020 08:05:55: 6000000 INFO @ Tue, 16 Jun 2020 08:05:56: 11000000 INFO @ Tue, 16 Jun 2020 08:06:01: 2000000 INFO @ Tue, 16 Jun 2020 08:06:02: 7000000 INFO @ Tue, 16 Jun 2020 08:06:03: 12000000 INFO @ Tue, 16 Jun 2020 08:06:06: 3000000 INFO @ Tue, 16 Jun 2020 08:06:08: 8000000 INFO @ Tue, 16 Jun 2020 08:06:09: 13000000 INFO @ Tue, 16 Jun 2020 08:06:12: 4000000 INFO @ Tue, 16 Jun 2020 08:06:14: 9000000 INFO @ Tue, 16 Jun 2020 08:06:15: 14000000 INFO @ Tue, 16 Jun 2020 08:06:18: 5000000 INFO @ Tue, 16 Jun 2020 08:06:20: 10000000 INFO @ Tue, 16 Jun 2020 08:06:21: 15000000 INFO @ Tue, 16 Jun 2020 08:06:23: 6000000 INFO @ Tue, 16 Jun 2020 08:06:26: 11000000 INFO @ Tue, 16 Jun 2020 08:06:27: 16000000 INFO @ Tue, 16 Jun 2020 08:06:29: 7000000 INFO @ Tue, 16 Jun 2020 08:06:32: 12000000 INFO @ Tue, 16 Jun 2020 08:06:33: 17000000 INFO @ Tue, 16 Jun 2020 08:06:34: 8000000 INFO @ Tue, 16 Jun 2020 08:06:38: 13000000 INFO @ Tue, 16 Jun 2020 08:06:39: 18000000 INFO @ Tue, 16 Jun 2020 08:06:40: 9000000 INFO @ Tue, 16 Jun 2020 08:06:44: 14000000 INFO @ Tue, 16 Jun 2020 08:06:45: 19000000 INFO @ Tue, 16 Jun 2020 08:06:46: 10000000 INFO @ Tue, 16 Jun 2020 08:06:50: 15000000 INFO @ Tue, 16 Jun 2020 08:06:51: 20000000 INFO @ Tue, 16 Jun 2020 08:06:51: 11000000 INFO @ Tue, 16 Jun 2020 08:06:56: 16000000 INFO @ Tue, 16 Jun 2020 08:06:57: 12000000 INFO @ Tue, 16 Jun 2020 08:06:57: 21000000 INFO @ Tue, 16 Jun 2020 08:07:02: 13000000 INFO @ Tue, 16 Jun 2020 08:07:02: 17000000 INFO @ Tue, 16 Jun 2020 08:07:03: 22000000 INFO @ Tue, 16 Jun 2020 08:07:08: 14000000 INFO @ Tue, 16 Jun 2020 08:07:08: 18000000 INFO @ Tue, 16 Jun 2020 08:07:09: 23000000 INFO @ Tue, 16 Jun 2020 08:07:13: 15000000 INFO @ Tue, 16 Jun 2020 08:07:14: 19000000 INFO @ Tue, 16 Jun 2020 08:07:15: 24000000 INFO @ Tue, 16 Jun 2020 08:07:19: 16000000 INFO @ Tue, 16 Jun 2020 08:07:20: 20000000 INFO @ Tue, 16 Jun 2020 08:07:21: 25000000 INFO @ Tue, 16 Jun 2020 08:07:24: 17000000 INFO @ Tue, 16 Jun 2020 08:07:26: 21000000 INFO @ Tue, 16 Jun 2020 08:07:27: 26000000 INFO @ Tue, 16 Jun 2020 08:07:30: 18000000 INFO @ Tue, 16 Jun 2020 08:07:33: 22000000 INFO @ Tue, 16 Jun 2020 08:07:33: 27000000 INFO @ Tue, 16 Jun 2020 08:07:35: #1 tag size is determined as 37 bps INFO @ Tue, 16 Jun 2020 08:07:35: #1 tag size = 37 INFO @ Tue, 16 Jun 2020 08:07:35: #1 total tags in treatment: 27306672 INFO @ Tue, 16 Jun 2020 08:07:35: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:07:35: #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 08:07:35: #1 tags after filtering in treatment: 27306672 INFO @ Tue, 16 Jun 2020 08:07:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:07:35: #1 finished! INFO @ Tue, 16 Jun 2020 08:07:35: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:07:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:07:36: 19000000 INFO @ Tue, 16 Jun 2020 08:07:37: #2 number of paired peaks: 122 WARNING @ Tue, 16 Jun 2020 08:07:37: Fewer paired peaks (122) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 122 pairs to build model! INFO @ Tue, 16 Jun 2020 08:07:37: start model_add_line... INFO @ Tue, 16 Jun 2020 08:07:37: start X-correlation... INFO @ Tue, 16 Jun 2020 08:07:37: end of X-cor INFO @ Tue, 16 Jun 2020 08:07:37: #2 finished! INFO @ Tue, 16 Jun 2020 08:07:37: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:07:37: #2 alternative fragment length(s) may be 1,30,479,547 bps INFO @ Tue, 16 Jun 2020 08:07:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059222/SRX059222.05_model.r WARNING @ Tue, 16 Jun 2020 08:07:37: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:07:37: #2 You may need to consider one of the other alternative d(s): 1,30,479,547 WARNING @ Tue, 16 Jun 2020 08:07:37: #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 08:07:37: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:07:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:07:39: 23000000 INFO @ Tue, 16 Jun 2020 08:07:41: 20000000 INFO @ Tue, 16 Jun 2020 08:07:45: 24000000 INFO @ Tue, 16 Jun 2020 08:07:47: 21000000 INFO @ Tue, 16 Jun 2020 08:07:51: 25000000 INFO @ Tue, 16 Jun 2020 08:07:53: 22000000 INFO @ Tue, 16 Jun 2020 08:07:57: 26000000 INFO @ Tue, 16 Jun 2020 08:07:58: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:08:02: 27000000 INFO @ Tue, 16 Jun 2020 08:08:04: 24000000 INFO @ Tue, 16 Jun 2020 08:08:04: #1 tag size is determined as 37 bps INFO @ Tue, 16 Jun 2020 08:08:04: #1 tag size = 37 INFO @ Tue, 16 Jun 2020 08:08:04: #1 total tags in treatment: 27306672 INFO @ Tue, 16 Jun 2020 08:08:04: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:08:04: #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 08:08:05: #1 tags after filtering in treatment: 27306672 INFO @ Tue, 16 Jun 2020 08:08:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:08:05: #1 finished! INFO @ Tue, 16 Jun 2020 08:08:05: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:08:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:08:06: #2 number of paired peaks: 122 WARNING @ Tue, 16 Jun 2020 08:08:06: Fewer paired peaks (122) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 122 pairs to build model! INFO @ Tue, 16 Jun 2020 08:08:06: start model_add_line... INFO @ Tue, 16 Jun 2020 08:08:07: start X-correlation... INFO @ Tue, 16 Jun 2020 08:08:07: end of X-cor INFO @ Tue, 16 Jun 2020 08:08:07: #2 finished! INFO @ Tue, 16 Jun 2020 08:08:07: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:08:07: #2 alternative fragment length(s) may be 1,30,479,547 bps INFO @ Tue, 16 Jun 2020 08:08:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059222/SRX059222.10_model.r WARNING @ Tue, 16 Jun 2020 08:08:07: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:08:07: #2 You may need to consider one of the other alternative d(s): 1,30,479,547 WARNING @ Tue, 16 Jun 2020 08:08:07: #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 08:08:07: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:08:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:08:09: 25000000 INFO @ Tue, 16 Jun 2020 08:08:15: 26000000 INFO @ Tue, 16 Jun 2020 08:08:17: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:08:21: 27000000 INFO @ Tue, 16 Jun 2020 08:08:23: #1 tag size is determined as 37 bps INFO @ Tue, 16 Jun 2020 08:08:23: #1 tag size = 37 INFO @ Tue, 16 Jun 2020 08:08:23: #1 total tags in treatment: 27306672 INFO @ Tue, 16 Jun 2020 08:08:23: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:08:23: #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 08:08:23: #1 tags after filtering in treatment: 27306672 INFO @ Tue, 16 Jun 2020 08:08:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:08:23: #1 finished! INFO @ Tue, 16 Jun 2020 08:08:23: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:08:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:08:25: #2 number of paired peaks: 122 WARNING @ Tue, 16 Jun 2020 08:08:25: Fewer paired peaks (122) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 122 pairs to build model! INFO @ Tue, 16 Jun 2020 08:08:25: start model_add_line... INFO @ Tue, 16 Jun 2020 08:08:25: start X-correlation... INFO @ Tue, 16 Jun 2020 08:08:25: end of X-cor INFO @ Tue, 16 Jun 2020 08:08:25: #2 finished! INFO @ Tue, 16 Jun 2020 08:08:25: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:08:25: #2 alternative fragment length(s) may be 1,30,479,547 bps INFO @ Tue, 16 Jun 2020 08:08:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059222/SRX059222.20_model.r WARNING @ Tue, 16 Jun 2020 08:08:25: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:08:25: #2 You may need to consider one of the other alternative d(s): 1,30,479,547 WARNING @ Tue, 16 Jun 2020 08:08:25: #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 08:08:25: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:08:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:08:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059222/SRX059222.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:08:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059222/SRX059222.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:08:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059222/SRX059222.05_summits.bed INFO @ Tue, 16 Jun 2020 08:08:36: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:08:48: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:09:06: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:09:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059222/SRX059222.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:09:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059222/SRX059222.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:09:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059222/SRX059222.10_summits.bed INFO @ Tue, 16 Jun 2020 08:09:07: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:09:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059222/SRX059222.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:09:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059222/SRX059222.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:09:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059222/SRX059222.20_summits.bed INFO @ Tue, 16 Jun 2020 08:09:24: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling