Job ID = 6507851 SRX = SRX494935 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T13:50:26 prefetch.2.10.7: 1) Downloading 'SRR1198467'... 2020-06-26T13:50:26 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:53:31 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:53:31 prefetch.2.10.7: 1) 'SRR1198467' was downloaded successfully Read 32317902 spots for SRR1198467/SRR1198467.sra Written 32317902 spots for SRR1198467/SRR1198467.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:46 32317902 reads; of these: 32317902 (100.00%) were unpaired; of these: 1919044 (5.94%) aligned 0 times 24975583 (77.28%) aligned exactly 1 time 5423275 (16.78%) aligned >1 times 94.06% overall alignment rate Time searching: 00:07:47 Overall time: 00:07:47 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 16 files... [bam_rmdupse_core] 5472006 / 30398858 = 0.1800 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 23:10:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494935/SRX494935.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494935/SRX494935.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494935/SRX494935.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494935/SRX494935.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 23:10:56: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:10:56: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:11:03: 1000000 INFO @ Fri, 26 Jun 2020 23:11:09: 2000000 INFO @ Fri, 26 Jun 2020 23:11:16: 3000000 INFO @ Fri, 26 Jun 2020 23:11:22: 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 23:11:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494935/SRX494935.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494935/SRX494935.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494935/SRX494935.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494935/SRX494935.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 23:11:26: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:11:26: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:11:28: 5000000 INFO @ Fri, 26 Jun 2020 23:11:34: 1000000 INFO @ Fri, 26 Jun 2020 23:11:35: 6000000 INFO @ Fri, 26 Jun 2020 23:11:40: 2000000 INFO @ Fri, 26 Jun 2020 23:11:42: 7000000 INFO @ Fri, 26 Jun 2020 23:11:47: 3000000 INFO @ Fri, 26 Jun 2020 23:11:49: 8000000 INFO @ Fri, 26 Jun 2020 23:11:54: 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 @ Fri, 26 Jun 2020 23:11:56: 9000000 INFO @ Fri, 26 Jun 2020 23:11:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX494935/SRX494935.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX494935/SRX494935.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX494935/SRX494935.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX494935/SRX494935.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 23:11:56: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:11:56: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:12:01: 5000000 INFO @ Fri, 26 Jun 2020 23:12:03: 10000000 INFO @ Fri, 26 Jun 2020 23:12:04: 1000000 INFO @ Fri, 26 Jun 2020 23:12:08: 6000000 INFO @ Fri, 26 Jun 2020 23:12:10: 11000000 INFO @ Fri, 26 Jun 2020 23:12:11: 2000000 INFO @ Fri, 26 Jun 2020 23:12:15: 7000000 INFO @ Fri, 26 Jun 2020 23:12:17: 12000000 INFO @ Fri, 26 Jun 2020 23:12:18: 3000000 INFO @ Fri, 26 Jun 2020 23:12:22: 8000000 INFO @ Fri, 26 Jun 2020 23:12:24: 13000000 INFO @ Fri, 26 Jun 2020 23:12:25: 4000000 INFO @ Fri, 26 Jun 2020 23:12:29: 9000000 INFO @ Fri, 26 Jun 2020 23:12:31: 14000000 INFO @ Fri, 26 Jun 2020 23:12:32: 5000000 INFO @ Fri, 26 Jun 2020 23:12:36: 10000000 INFO @ Fri, 26 Jun 2020 23:12:38: 15000000 INFO @ Fri, 26 Jun 2020 23:12:39: 6000000 INFO @ Fri, 26 Jun 2020 23:12:43: 11000000 INFO @ Fri, 26 Jun 2020 23:12:45: 16000000 INFO @ Fri, 26 Jun 2020 23:12:46: 7000000 INFO @ Fri, 26 Jun 2020 23:12:50: 12000000 INFO @ Fri, 26 Jun 2020 23:12:52: 17000000 INFO @ Fri, 26 Jun 2020 23:12:53: 8000000 INFO @ Fri, 26 Jun 2020 23:12:57: 13000000 INFO @ Fri, 26 Jun 2020 23:12:59: 18000000 INFO @ Fri, 26 Jun 2020 23:13:00: 9000000 INFO @ Fri, 26 Jun 2020 23:13:04: 14000000 INFO @ Fri, 26 Jun 2020 23:13:07: 19000000 INFO @ Fri, 26 Jun 2020 23:13:08: 10000000 INFO @ Fri, 26 Jun 2020 23:13:11: 15000000 INFO @ Fri, 26 Jun 2020 23:13:14: 20000000 INFO @ Fri, 26 Jun 2020 23:13:15: 11000000 INFO @ Fri, 26 Jun 2020 23:13:18: 16000000 INFO @ Fri, 26 Jun 2020 23:13:21: 21000000 INFO @ Fri, 26 Jun 2020 23:13:22: 12000000 INFO @ Fri, 26 Jun 2020 23:13:25: 17000000 INFO @ Fri, 26 Jun 2020 23:13:28: 22000000 INFO @ Fri, 26 Jun 2020 23:13:29: 13000000 INFO @ Fri, 26 Jun 2020 23:13:32: 18000000 INFO @ Fri, 26 Jun 2020 23:13:35: 23000000 INFO @ Fri, 26 Jun 2020 23:13:36: 14000000 INFO @ Fri, 26 Jun 2020 23:13:39: 19000000 INFO @ Fri, 26 Jun 2020 23:13:42: 24000000 INFO @ Fri, 26 Jun 2020 23:13:43: 15000000 INFO @ Fri, 26 Jun 2020 23:13:46: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 23:13:48: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:13:48: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:13:48: #1 total tags in treatment: 24926852 INFO @ Fri, 26 Jun 2020 23:13:48: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:13:48: #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 23:13:49: #1 tags after filtering in treatment: 24926852 INFO @ Fri, 26 Jun 2020 23:13:49: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:13:49: #1 finished! INFO @ Fri, 26 Jun 2020 23:13:49: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:13:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:13:50: 16000000 INFO @ Fri, 26 Jun 2020 23:13:51: #2 number of paired peaks: 128 WARNING @ Fri, 26 Jun 2020 23:13:51: Fewer paired peaks (128) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 128 pairs to build model! INFO @ Fri, 26 Jun 2020 23:13:51: start model_add_line... INFO @ Fri, 26 Jun 2020 23:13:51: start X-correlation... INFO @ Fri, 26 Jun 2020 23:13:51: end of X-cor INFO @ Fri, 26 Jun 2020 23:13:51: #2 finished! INFO @ Fri, 26 Jun 2020 23:13:51: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 23:13:51: #2 alternative fragment length(s) may be 1,27,578 bps INFO @ Fri, 26 Jun 2020 23:13:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494935/SRX494935.05_model.r WARNING @ Fri, 26 Jun 2020 23:13:51: #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 23:13:51: #2 You may need to consider one of the other alternative d(s): 1,27,578 WARNING @ Fri, 26 Jun 2020 23:13:51: #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 23:13:51: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:13:51: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:13:53: 21000000 INFO @ Fri, 26 Jun 2020 23:13:56: 17000000 INFO @ Fri, 26 Jun 2020 23:14:00: 22000000 INFO @ Fri, 26 Jun 2020 23:14:03: 18000000 INFO @ Fri, 26 Jun 2020 23:14:06: 23000000 INFO @ Fri, 26 Jun 2020 23:14:10: 19000000 INFO @ Fri, 26 Jun 2020 23:14:13: 24000000 INFO @ Fri, 26 Jun 2020 23:14:17: 20000000 INFO @ Fri, 26 Jun 2020 23:14:20: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:14:20: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:14:20: #1 total tags in treatment: 24926852 INFO @ Fri, 26 Jun 2020 23:14:20: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:14:20: #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 23:14:20: #1 tags after filtering in treatment: 24926852 INFO @ Fri, 26 Jun 2020 23:14:20: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:14:20: #1 finished! INFO @ Fri, 26 Jun 2020 23:14:20: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:14:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:14:22: #2 number of paired peaks: 128 WARNING @ Fri, 26 Jun 2020 23:14:22: Fewer paired peaks (128) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 128 pairs to build model! INFO @ Fri, 26 Jun 2020 23:14:22: start model_add_line... INFO @ Fri, 26 Jun 2020 23:14:22: start X-correlation... INFO @ Fri, 26 Jun 2020 23:14:22: end of X-cor INFO @ Fri, 26 Jun 2020 23:14:22: #2 finished! INFO @ Fri, 26 Jun 2020 23:14:22: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 23:14:22: #2 alternative fragment length(s) may be 1,27,578 bps INFO @ Fri, 26 Jun 2020 23:14:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494935/SRX494935.10_model.r WARNING @ Fri, 26 Jun 2020 23:14:22: #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 23:14:22: #2 You may need to consider one of the other alternative d(s): 1,27,578 WARNING @ Fri, 26 Jun 2020 23:14:22: #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 23:14:22: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:14:22: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:14:23: 21000000 INFO @ Fri, 26 Jun 2020 23:14:28: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:14:30: 22000000 INFO @ Fri, 26 Jun 2020 23:14:36: 23000000 INFO @ Fri, 26 Jun 2020 23:14:42: 24000000 BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 23:14:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494935/SRX494935.05_peaks.xls INFO @ Fri, 26 Jun 2020 23:14:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494935/SRX494935.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:14:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494935/SRX494935.05_summits.bed INFO @ Fri, 26 Jun 2020 23:14:46: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:14:48: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:14:48: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:14:48: #1 total tags in treatment: 24926852 INFO @ Fri, 26 Jun 2020 23:14:48: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:14:48: #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 23:14:48: #1 tags after filtering in treatment: 24926852 INFO @ Fri, 26 Jun 2020 23:14:48: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 23:14:48: #1 finished! INFO @ Fri, 26 Jun 2020 23:14:48: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:14:48: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:14:50: #2 number of paired peaks: 128 WARNING @ Fri, 26 Jun 2020 23:14:50: Fewer paired peaks (128) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 128 pairs to build model! INFO @ Fri, 26 Jun 2020 23:14:50: start model_add_line... INFO @ Fri, 26 Jun 2020 23:14:50: start X-correlation... INFO @ Fri, 26 Jun 2020 23:14:50: end of X-cor INFO @ Fri, 26 Jun 2020 23:14:50: #2 finished! INFO @ Fri, 26 Jun 2020 23:14:50: #2 predicted fragment length is 1 bps INFO @ Fri, 26 Jun 2020 23:14:50: #2 alternative fragment length(s) may be 1,27,578 bps INFO @ Fri, 26 Jun 2020 23:14:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX494935/SRX494935.20_model.r WARNING @ Fri, 26 Jun 2020 23:14:50: #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 23:14:50: #2 You may need to consider one of the other alternative d(s): 1,27,578 WARNING @ Fri, 26 Jun 2020 23:14:50: #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 23:14:50: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:14:50: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:14:58: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:15:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494935/SRX494935.10_peaks.xls INFO @ Fri, 26 Jun 2020 23:15:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494935/SRX494935.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:15:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494935/SRX494935.10_summits.bed INFO @ Fri, 26 Jun 2020 23:15:15: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:15:27: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:15:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX494935/SRX494935.20_peaks.xls INFO @ Fri, 26 Jun 2020 23:15:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX494935/SRX494935.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:15:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX494935/SRX494935.20_summits.bed INFO @ Fri, 26 Jun 2020 23:15:44: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling