Job ID = 6366721 SRX = SRX2228874 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:01:23 prefetch.2.10.7: 1) Downloading 'SRR4380330'... 2020-06-15T23:01:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:03:11 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:03:11 prefetch.2.10.7: 1) 'SRR4380330' was downloaded successfully 2020-06-15T23:03:12 prefetch.2.10.7: 'SRR4380330' has 0 unresolved dependencies Read 33038431 spots for SRR4380330/SRR4380330.sra Written 33038431 spots for SRR4380330/SRR4380330.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: 00:05:47 33038431 reads; of these: 33038431 (100.00%) were unpaired; of these: 12099573 (36.62%) aligned 0 times 17142931 (51.89%) aligned exactly 1 time 3795927 (11.49%) aligned >1 times 63.38% overall alignment rate Time searching: 00:05:47 Overall time: 00:05:47 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 12 files... [bam_rmdupse_core] 4439811 / 20938858 = 0.2120 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 08:15:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228874/SRX2228874.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228874/SRX2228874.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228874/SRX2228874.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228874/SRX2228874.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 08:15:45: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:15:45: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:15:51: 1000000 INFO @ Tue, 16 Jun 2020 08:15:58: 2000000 INFO @ Tue, 16 Jun 2020 08:16:04: 3000000 INFO @ Tue, 16 Jun 2020 08:16:10: 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 08:16:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228874/SRX2228874.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228874/SRX2228874.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228874/SRX2228874.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228874/SRX2228874.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 08:16:15: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:16:15: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:16:16: 5000000 INFO @ Tue, 16 Jun 2020 08:16:21: 1000000 INFO @ Tue, 16 Jun 2020 08:16:23: 6000000 INFO @ Tue, 16 Jun 2020 08:16:28: 2000000 INFO @ Tue, 16 Jun 2020 08:16:30: 7000000 INFO @ Tue, 16 Jun 2020 08:16:34: 3000000 INFO @ Tue, 16 Jun 2020 08:16:36: 8000000 INFO @ Tue, 16 Jun 2020 08:16:41: 4000000 BedGraph に変換中... INFO @ Tue, 16 Jun 2020 08:16:43: 9000000 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 08:16:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228874/SRX2228874.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228874/SRX2228874.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228874/SRX2228874.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228874/SRX2228874.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 08:16:45: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:16:45: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:16:48: 5000000 INFO @ Tue, 16 Jun 2020 08:16:49: 10000000 INFO @ Tue, 16 Jun 2020 08:16:51: 1000000 INFO @ Tue, 16 Jun 2020 08:16:54: 6000000 INFO @ Tue, 16 Jun 2020 08:16:56: 11000000 INFO @ Tue, 16 Jun 2020 08:16:57: 2000000 INFO @ Tue, 16 Jun 2020 08:17:01: 7000000 INFO @ Tue, 16 Jun 2020 08:17:03: 3000000 INFO @ Tue, 16 Jun 2020 08:17:03: 12000000 INFO @ Tue, 16 Jun 2020 08:17:08: 8000000 INFO @ Tue, 16 Jun 2020 08:17:09: 4000000 INFO @ Tue, 16 Jun 2020 08:17:10: 13000000 INFO @ Tue, 16 Jun 2020 08:17:14: 9000000 INFO @ Tue, 16 Jun 2020 08:17:15: 5000000 INFO @ Tue, 16 Jun 2020 08:17:16: 14000000 INFO @ Tue, 16 Jun 2020 08:17:21: 10000000 INFO @ Tue, 16 Jun 2020 08:17:21: 6000000 INFO @ Tue, 16 Jun 2020 08:17:23: 15000000 INFO @ Tue, 16 Jun 2020 08:17:27: 7000000 INFO @ Tue, 16 Jun 2020 08:17:27: 11000000 INFO @ Tue, 16 Jun 2020 08:17:29: 16000000 INFO @ Tue, 16 Jun 2020 08:17:33: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:17:33: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:17:33: #1 total tags in treatment: 16499047 INFO @ Tue, 16 Jun 2020 08:17:33: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:17:33: #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 08:17:33: 8000000 INFO @ Tue, 16 Jun 2020 08:17:33: #1 tags after filtering in treatment: 16499047 INFO @ Tue, 16 Jun 2020 08:17:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:17:33: #1 finished! INFO @ Tue, 16 Jun 2020 08:17:33: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:17:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:17:34: 12000000 INFO @ Tue, 16 Jun 2020 08:17:34: #2 number of paired peaks: 274 WARNING @ Tue, 16 Jun 2020 08:17:34: Fewer paired peaks (274) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 274 pairs to build model! INFO @ Tue, 16 Jun 2020 08:17:34: start model_add_line... INFO @ Tue, 16 Jun 2020 08:17:34: start X-correlation... INFO @ Tue, 16 Jun 2020 08:17:34: end of X-cor INFO @ Tue, 16 Jun 2020 08:17:34: #2 finished! INFO @ Tue, 16 Jun 2020 08:17:34: #2 predicted fragment length is 2 bps INFO @ Tue, 16 Jun 2020 08:17:34: #2 alternative fragment length(s) may be 2,41,548,573 bps INFO @ Tue, 16 Jun 2020 08:17:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228874/SRX2228874.05_model.r WARNING @ Tue, 16 Jun 2020 08:17:34: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:17:34: #2 You may need to consider one of the other alternative d(s): 2,41,548,573 WARNING @ Tue, 16 Jun 2020 08:17:34: #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 08:17:34: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:17:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:17:39: 9000000 INFO @ Tue, 16 Jun 2020 08:17:40: 13000000 INFO @ Tue, 16 Jun 2020 08:17:45: 10000000 INFO @ Tue, 16 Jun 2020 08:17:47: 14000000 INFO @ Tue, 16 Jun 2020 08:17:51: 11000000 INFO @ Tue, 16 Jun 2020 08:17:53: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:17:57: 12000000 INFO @ Tue, 16 Jun 2020 08:18:00: 16000000 INFO @ Tue, 16 Jun 2020 08:18:02: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:18:03: 13000000 INFO @ Tue, 16 Jun 2020 08:18:03: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:18:03: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:18:03: #1 total tags in treatment: 16499047 INFO @ Tue, 16 Jun 2020 08:18:03: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:18:03: #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 08:18:03: #1 tags after filtering in treatment: 16499047 INFO @ Tue, 16 Jun 2020 08:18:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:18:03: #1 finished! INFO @ Tue, 16 Jun 2020 08:18:03: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:18:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:18:04: #2 number of paired peaks: 274 WARNING @ Tue, 16 Jun 2020 08:18:04: Fewer paired peaks (274) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 274 pairs to build model! INFO @ Tue, 16 Jun 2020 08:18:04: start model_add_line... INFO @ Tue, 16 Jun 2020 08:18:04: start X-correlation... INFO @ Tue, 16 Jun 2020 08:18:04: end of X-cor INFO @ Tue, 16 Jun 2020 08:18:04: #2 finished! INFO @ Tue, 16 Jun 2020 08:18:04: #2 predicted fragment length is 2 bps INFO @ Tue, 16 Jun 2020 08:18:04: #2 alternative fragment length(s) may be 2,41,548,573 bps INFO @ Tue, 16 Jun 2020 08:18:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228874/SRX2228874.10_model.r WARNING @ Tue, 16 Jun 2020 08:18:04: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:18:04: #2 You may need to consider one of the other alternative d(s): 2,41,548,573 WARNING @ Tue, 16 Jun 2020 08:18:04: #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 08:18:04: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:18:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:18:08: 14000000 INFO @ Tue, 16 Jun 2020 08:18:13: 15000000 INFO @ Tue, 16 Jun 2020 08:18:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228874/SRX2228874.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:18:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228874/SRX2228874.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:18:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228874/SRX2228874.05_summits.bed INFO @ Tue, 16 Jun 2020 08:18:16: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:18:19: 16000000 INFO @ Tue, 16 Jun 2020 08:18:21: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:18:21: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:18:21: #1 total tags in treatment: 16499047 INFO @ Tue, 16 Jun 2020 08:18:21: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:18:21: #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 08:18:22: #1 tags after filtering in treatment: 16499047 INFO @ Tue, 16 Jun 2020 08:18:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:18:22: #1 finished! INFO @ Tue, 16 Jun 2020 08:18:22: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:18:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:18:23: #2 number of paired peaks: 274 WARNING @ Tue, 16 Jun 2020 08:18:23: Fewer paired peaks (274) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 274 pairs to build model! INFO @ Tue, 16 Jun 2020 08:18:23: start model_add_line... INFO @ Tue, 16 Jun 2020 08:18:23: start X-correlation... INFO @ Tue, 16 Jun 2020 08:18:23: end of X-cor INFO @ Tue, 16 Jun 2020 08:18:23: #2 finished! INFO @ Tue, 16 Jun 2020 08:18:23: #2 predicted fragment length is 2 bps INFO @ Tue, 16 Jun 2020 08:18:23: #2 alternative fragment length(s) may be 2,41,548,573 bps INFO @ Tue, 16 Jun 2020 08:18:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228874/SRX2228874.20_model.r WARNING @ Tue, 16 Jun 2020 08:18:23: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:18:23: #2 You may need to consider one of the other alternative d(s): 2,41,548,573 WARNING @ Tue, 16 Jun 2020 08:18:23: #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 08:18:23: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:18:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:18:32: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:18:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228874/SRX2228874.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:18:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228874/SRX2228874.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:18:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228874/SRX2228874.10_summits.bed INFO @ Tue, 16 Jun 2020 08:18:45: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:18:50: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:19:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228874/SRX2228874.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:19:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228874/SRX2228874.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:19:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228874/SRX2228874.20_summits.bed INFO @ Tue, 16 Jun 2020 08:19:04: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling