Job ID = 5720206 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 32,861,226 reads read : 65,722,452 reads written : 32,861,226 reads 0-length : 32,861,226 rm: cannot remove ‘[DSE]RR*’: No such file or directory 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 32861226 reads; of these: 32861226 (100.00%) were unpaired; of these: 2438663 (7.42%) aligned 0 times 25631582 (78.00%) aligned exactly 1 time 4790981 (14.58%) aligned >1 times 92.58% 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 16 files... [bam_rmdupse_core] 5356518 / 30422563 = 0.1761 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 @ Wed, 15 Apr 2020 21:52:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6619574/SRX6619574.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6619574/SRX6619574.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6619574/SRX6619574.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6619574/SRX6619574.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 @ Wed, 15 Apr 2020 21:52:37: #1 read tag files... INFO @ Wed, 15 Apr 2020 21:52:37: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 21:52:42: 1000000 INFO @ Wed, 15 Apr 2020 21:52:47: 2000000 INFO @ Wed, 15 Apr 2020 21:52:52: 3000000 INFO @ Wed, 15 Apr 2020 21:52:57: 4000000 INFO @ Wed, 15 Apr 2020 21:53:02: 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 @ Wed, 15 Apr 2020 21:53:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6619574/SRX6619574.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6619574/SRX6619574.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6619574/SRX6619574.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6619574/SRX6619574.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 @ Wed, 15 Apr 2020 21:53:07: #1 read tag files... INFO @ Wed, 15 Apr 2020 21:53:07: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 21:53:07: 6000000 INFO @ Wed, 15 Apr 2020 21:53:12: 1000000 INFO @ Wed, 15 Apr 2020 21:53:12: 7000000 INFO @ Wed, 15 Apr 2020 21:53:18: 2000000 INFO @ Wed, 15 Apr 2020 21:53:18: 8000000 INFO @ Wed, 15 Apr 2020 21:53:23: 9000000 INFO @ Wed, 15 Apr 2020 21:53:23: 3000000 INFO @ Wed, 15 Apr 2020 21:53:28: 10000000 INFO @ Wed, 15 Apr 2020 21:53:28: 4000000 INFO @ Wed, 15 Apr 2020 21:53:34: 5000000 INFO @ Wed, 15 Apr 2020 21:53:34: 11000000 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 @ Wed, 15 Apr 2020 21:53:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6619574/SRX6619574.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6619574/SRX6619574.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6619574/SRX6619574.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6619574/SRX6619574.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 @ Wed, 15 Apr 2020 21:53:37: #1 read tag files... INFO @ Wed, 15 Apr 2020 21:53:37: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 21:53:39: 6000000 INFO @ Wed, 15 Apr 2020 21:53:39: 12000000 INFO @ Wed, 15 Apr 2020 21:53:43: 1000000 INFO @ Wed, 15 Apr 2020 21:53:45: 7000000 INFO @ Wed, 15 Apr 2020 21:53:45: 13000000 INFO @ Wed, 15 Apr 2020 21:53:48: 2000000 INFO @ Wed, 15 Apr 2020 21:53:50: 8000000 INFO @ Wed, 15 Apr 2020 21:53:50: 14000000 INFO @ Wed, 15 Apr 2020 21:53:54: 3000000 INFO @ Wed, 15 Apr 2020 21:53:55: 9000000 INFO @ Wed, 15 Apr 2020 21:53:56: 15000000 INFO @ Wed, 15 Apr 2020 21:53:59: 4000000 INFO @ Wed, 15 Apr 2020 21:54:01: 10000000 INFO @ Wed, 15 Apr 2020 21:54:01: 16000000 INFO @ Wed, 15 Apr 2020 21:54:05: 5000000 INFO @ Wed, 15 Apr 2020 21:54:06: 11000000 INFO @ Wed, 15 Apr 2020 21:54:07: 17000000 INFO @ Wed, 15 Apr 2020 21:54:10: 6000000 INFO @ Wed, 15 Apr 2020 21:54:12: 12000000 INFO @ Wed, 15 Apr 2020 21:54:12: 18000000 INFO @ Wed, 15 Apr 2020 21:54:15: 7000000 INFO @ Wed, 15 Apr 2020 21:54:17: 13000000 INFO @ Wed, 15 Apr 2020 21:54:17: 19000000 INFO @ Wed, 15 Apr 2020 21:54:20: 8000000 INFO @ Wed, 15 Apr 2020 21:54:22: 14000000 INFO @ Wed, 15 Apr 2020 21:54:23: 20000000 INFO @ Wed, 15 Apr 2020 21:54:26: 9000000 INFO @ Wed, 15 Apr 2020 21:54:28: 15000000 INFO @ Wed, 15 Apr 2020 21:54:28: 21000000 INFO @ Wed, 15 Apr 2020 21:54:31: 10000000 INFO @ Wed, 15 Apr 2020 21:54:33: 16000000 INFO @ Wed, 15 Apr 2020 21:54:34: 22000000 INFO @ Wed, 15 Apr 2020 21:54:37: 11000000 INFO @ Wed, 15 Apr 2020 21:54:39: 17000000 INFO @ Wed, 15 Apr 2020 21:54:39: 23000000 INFO @ Wed, 15 Apr 2020 21:54:42: 12000000 INFO @ Wed, 15 Apr 2020 21:54:44: 18000000 INFO @ Wed, 15 Apr 2020 21:54:44: 24000000 INFO @ Wed, 15 Apr 2020 21:54:47: 13000000 INFO @ Wed, 15 Apr 2020 21:54:50: 19000000 INFO @ Wed, 15 Apr 2020 21:54:50: 25000000 INFO @ Wed, 15 Apr 2020 21:54:50: #1 tag size is determined as 50 bps INFO @ Wed, 15 Apr 2020 21:54:50: #1 tag size = 50 INFO @ Wed, 15 Apr 2020 21:54:50: #1 total tags in treatment: 25066045 INFO @ Wed, 15 Apr 2020 21:54:50: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 21:54:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 15 Apr 2020 21:54:51: #1 tags after filtering in treatment: 25066045 INFO @ Wed, 15 Apr 2020 21:54:51: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 21:54:51: #1 finished! INFO @ Wed, 15 Apr 2020 21:54:51: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 21:54:51: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 21:54:52: #2 number of paired peaks: 142 WARNING @ Wed, 15 Apr 2020 21:54:52: Fewer paired peaks (142) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 142 pairs to build model! INFO @ Wed, 15 Apr 2020 21:54:52: start model_add_line... INFO @ Wed, 15 Apr 2020 21:54:52: start X-correlation... INFO @ Wed, 15 Apr 2020 21:54:52: end of X-cor INFO @ Wed, 15 Apr 2020 21:54:52: #2 finished! INFO @ Wed, 15 Apr 2020 21:54:52: #2 predicted fragment length is 1 bps INFO @ Wed, 15 Apr 2020 21:54:52: #2 alternative fragment length(s) may be 1,43,564,588 bps INFO @ Wed, 15 Apr 2020 21:54:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6619574/SRX6619574.05_model.r WARNING @ Wed, 15 Apr 2020 21:54:52: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 15 Apr 2020 21:54:52: #2 You may need to consider one of the other alternative d(s): 1,43,564,588 WARNING @ Wed, 15 Apr 2020 21:54:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 15 Apr 2020 21:54:52: #3 Call peaks... INFO @ Wed, 15 Apr 2020 21:54:52: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 21:54:53: 14000000 INFO @ Wed, 15 Apr 2020 21:54:55: 20000000 INFO @ Wed, 15 Apr 2020 21:54:58: 15000000 INFO @ Wed, 15 Apr 2020 21:55:00: 21000000 INFO @ Wed, 15 Apr 2020 21:55:03: 16000000 INFO @ Wed, 15 Apr 2020 21:55:06: 22000000 INFO @ Wed, 15 Apr 2020 21:55:09: 17000000 INFO @ Wed, 15 Apr 2020 21:55:11: 23000000 INFO @ Wed, 15 Apr 2020 21:55:14: 18000000 INFO @ Wed, 15 Apr 2020 21:55:17: 24000000 INFO @ Wed, 15 Apr 2020 21:55:20: 19000000 INFO @ Wed, 15 Apr 2020 21:55:22: 25000000 INFO @ Wed, 15 Apr 2020 21:55:22: #1 tag size is determined as 50 bps INFO @ Wed, 15 Apr 2020 21:55:22: #1 tag size = 50 INFO @ Wed, 15 Apr 2020 21:55:22: #1 total tags in treatment: 25066045 INFO @ Wed, 15 Apr 2020 21:55:22: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 21:55:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 15 Apr 2020 21:55:23: #1 tags after filtering in treatment: 25066045 INFO @ Wed, 15 Apr 2020 21:55:23: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 21:55:23: #1 finished! INFO @ Wed, 15 Apr 2020 21:55:23: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 21:55:23: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 21:55:24: #2 number of paired peaks: 142 WARNING @ Wed, 15 Apr 2020 21:55:24: Fewer paired peaks (142) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 142 pairs to build model! INFO @ Wed, 15 Apr 2020 21:55:24: start model_add_line... INFO @ Wed, 15 Apr 2020 21:55:24: start X-correlation... INFO @ Wed, 15 Apr 2020 21:55:24: end of X-cor INFO @ Wed, 15 Apr 2020 21:55:24: #2 finished! INFO @ Wed, 15 Apr 2020 21:55:24: #2 predicted fragment length is 1 bps INFO @ Wed, 15 Apr 2020 21:55:24: #2 alternative fragment length(s) may be 1,43,564,588 bps INFO @ Wed, 15 Apr 2020 21:55:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6619574/SRX6619574.10_model.r WARNING @ Wed, 15 Apr 2020 21:55:24: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 15 Apr 2020 21:55:24: #2 You may need to consider one of the other alternative d(s): 1,43,564,588 WARNING @ Wed, 15 Apr 2020 21:55:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 15 Apr 2020 21:55:24: #3 Call peaks... INFO @ Wed, 15 Apr 2020 21:55:24: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 21:55:25: 20000000 INFO @ Wed, 15 Apr 2020 21:55:27: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 21:55:30: 21000000 INFO @ Wed, 15 Apr 2020 21:55:35: 22000000 INFO @ Wed, 15 Apr 2020 21:55:40: 23000000 INFO @ Wed, 15 Apr 2020 21:55:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6619574/SRX6619574.05_peaks.xls INFO @ Wed, 15 Apr 2020 21:55:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6619574/SRX6619574.05_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 21:55:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6619574/SRX6619574.05_summits.bed INFO @ Wed, 15 Apr 2020 21:55:43: Done! INFO @ Wed, 15 Apr 2020 21:55:45: 24000000 pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 15 Apr 2020 21:55:50: 25000000 INFO @ Wed, 15 Apr 2020 21:55:51: #1 tag size is determined as 50 bps INFO @ Wed, 15 Apr 2020 21:55:51: #1 tag size = 50 INFO @ Wed, 15 Apr 2020 21:55:51: #1 total tags in treatment: 25066045 INFO @ Wed, 15 Apr 2020 21:55:51: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 21:55:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 15 Apr 2020 21:55:51: #1 tags after filtering in treatment: 25066045 INFO @ Wed, 15 Apr 2020 21:55:51: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 21:55:51: #1 finished! INFO @ Wed, 15 Apr 2020 21:55:51: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 21:55:51: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 21:55:53: #2 number of paired peaks: 142 WARNING @ Wed, 15 Apr 2020 21:55:53: Fewer paired peaks (142) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 142 pairs to build model! INFO @ Wed, 15 Apr 2020 21:55:53: start model_add_line... INFO @ Wed, 15 Apr 2020 21:55:53: start X-correlation... INFO @ Wed, 15 Apr 2020 21:55:53: end of X-cor INFO @ Wed, 15 Apr 2020 21:55:53: #2 finished! INFO @ Wed, 15 Apr 2020 21:55:53: #2 predicted fragment length is 1 bps INFO @ Wed, 15 Apr 2020 21:55:53: #2 alternative fragment length(s) may be 1,43,564,588 bps INFO @ Wed, 15 Apr 2020 21:55:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6619574/SRX6619574.20_model.r WARNING @ Wed, 15 Apr 2020 21:55:53: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 15 Apr 2020 21:55:53: #2 You may need to consider one of the other alternative d(s): 1,43,564,588 WARNING @ Wed, 15 Apr 2020 21:55:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 15 Apr 2020 21:55:53: #3 Call peaks... INFO @ Wed, 15 Apr 2020 21:55:53: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 21:56:01: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 21:56:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6619574/SRX6619574.10_peaks.xls INFO @ Wed, 15 Apr 2020 21:56:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6619574/SRX6619574.10_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 21:56:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6619574/SRX6619574.10_summits.bed INFO @ Wed, 15 Apr 2020 21:56:17: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 15 Apr 2020 21:56:29: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 21:56:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6619574/SRX6619574.20_peaks.xls INFO @ Wed, 15 Apr 2020 21:56:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6619574/SRX6619574.20_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 21:56:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6619574/SRX6619574.20_summits.bed INFO @ Wed, 15 Apr 2020 21:56:45: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。