Job ID = 6369031 SRX = SRX982096 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:41:14 prefetch.2.10.7: 1) Downloading 'SRR1956583'... 2020-06-16T00:41:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:45:00 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:45:00 prefetch.2.10.7: 'SRR1956583' is valid 2020-06-16T00:45:00 prefetch.2.10.7: 1) 'SRR1956583' was downloaded successfully Read 12516168 spots for SRR1956583/SRR1956583.sra Written 12516168 spots for SRR1956583/SRR1956583.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: 00:02:56 12516168 reads; of these: 12516168 (100.00%) were unpaired; of these: 236594 (1.89%) aligned 0 times 10352013 (82.71%) aligned exactly 1 time 1927561 (15.40%) aligned >1 times 98.11% overall alignment rate Time searching: 00:02:56 Overall time: 00:02:56 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] 887846 / 12279574 = 0.0723 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 09:52:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982096/SRX982096.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982096/SRX982096.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982096/SRX982096.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982096/SRX982096.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 09:52:16: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:52:16: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:52:22: 1000000 INFO @ Tue, 16 Jun 2020 09:52:28: 2000000 INFO @ Tue, 16 Jun 2020 09:52:33: 3000000 INFO @ Tue, 16 Jun 2020 09:52:39: 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 09:52:45: 5000000 INFO @ Tue, 16 Jun 2020 09:52:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982096/SRX982096.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982096/SRX982096.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982096/SRX982096.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982096/SRX982096.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 09:52:46: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:52:46: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:52:51: 6000000 INFO @ Tue, 16 Jun 2020 09:52:54: 1000000 INFO @ Tue, 16 Jun 2020 09:52:58: 7000000 INFO @ Tue, 16 Jun 2020 09:53:01: 2000000 INFO @ Tue, 16 Jun 2020 09:53:05: 8000000 INFO @ Tue, 16 Jun 2020 09:53:09: 3000000 INFO @ Tue, 16 Jun 2020 09:53:11: 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 09:53:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982096/SRX982096.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982096/SRX982096.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982096/SRX982096.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982096/SRX982096.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 09:53:16: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:53:16: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:53:16: 4000000 INFO @ Tue, 16 Jun 2020 09:53:19: 10000000 INFO @ Tue, 16 Jun 2020 09:53:23: 1000000 INFO @ Tue, 16 Jun 2020 09:53:24: 5000000 INFO @ Tue, 16 Jun 2020 09:53:26: 11000000 INFO @ Tue, 16 Jun 2020 09:53:28: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:53:28: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:53:28: #1 total tags in treatment: 11391728 INFO @ Tue, 16 Jun 2020 09:53:28: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:53:28: #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 09:53:29: #1 tags after filtering in treatment: 11391728 INFO @ Tue, 16 Jun 2020 09:53:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:53:29: #1 finished! INFO @ Tue, 16 Jun 2020 09:53:29: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:53:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:53:29: #2 number of paired peaks: 271 WARNING @ Tue, 16 Jun 2020 09:53:29: Fewer paired peaks (271) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 271 pairs to build model! INFO @ Tue, 16 Jun 2020 09:53:29: start model_add_line... INFO @ Tue, 16 Jun 2020 09:53:29: start X-correlation... INFO @ Tue, 16 Jun 2020 09:53:29: end of X-cor INFO @ Tue, 16 Jun 2020 09:53:29: #2 finished! INFO @ Tue, 16 Jun 2020 09:53:29: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 09:53:29: #2 alternative fragment length(s) may be 2,49,563 bps INFO @ Tue, 16 Jun 2020 09:53:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982096/SRX982096.05_model.r WARNING @ Tue, 16 Jun 2020 09:53:29: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:53:29: #2 You may need to consider one of the other alternative d(s): 2,49,563 WARNING @ Tue, 16 Jun 2020 09:53:29: #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 09:53:29: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:53:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:53:30: 2000000 INFO @ Tue, 16 Jun 2020 09:53:31: 6000000 INFO @ Tue, 16 Jun 2020 09:53:37: 3000000 INFO @ Tue, 16 Jun 2020 09:53:39: 7000000 INFO @ Tue, 16 Jun 2020 09:53:44: 4000000 INFO @ Tue, 16 Jun 2020 09:53:46: 8000000 INFO @ Tue, 16 Jun 2020 09:53:51: 5000000 INFO @ Tue, 16 Jun 2020 09:53:52: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:53:54: 9000000 INFO @ Tue, 16 Jun 2020 09:53:57: 6000000 INFO @ Tue, 16 Jun 2020 09:54:02: 10000000 INFO @ Tue, 16 Jun 2020 09:54:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982096/SRX982096.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:54:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982096/SRX982096.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:54:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982096/SRX982096.05_summits.bed INFO @ Tue, 16 Jun 2020 09:54:03: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (563 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:54:04: 7000000 INFO @ Tue, 16 Jun 2020 09:54:10: 11000000 INFO @ Tue, 16 Jun 2020 09:54:10: 8000000 INFO @ Tue, 16 Jun 2020 09:54:12: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:54:12: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:54:12: #1 total tags in treatment: 11391728 INFO @ Tue, 16 Jun 2020 09:54:12: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:54:12: #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 09:54:13: #1 tags after filtering in treatment: 11391728 INFO @ Tue, 16 Jun 2020 09:54:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:54:13: #1 finished! INFO @ Tue, 16 Jun 2020 09:54:13: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:54:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:54:13: #2 number of paired peaks: 271 WARNING @ Tue, 16 Jun 2020 09:54:13: Fewer paired peaks (271) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 271 pairs to build model! INFO @ Tue, 16 Jun 2020 09:54:13: start model_add_line... INFO @ Tue, 16 Jun 2020 09:54:14: start X-correlation... INFO @ Tue, 16 Jun 2020 09:54:14: end of X-cor INFO @ Tue, 16 Jun 2020 09:54:14: #2 finished! INFO @ Tue, 16 Jun 2020 09:54:14: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 09:54:14: #2 alternative fragment length(s) may be 2,49,563 bps INFO @ Tue, 16 Jun 2020 09:54:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982096/SRX982096.10_model.r WARNING @ Tue, 16 Jun 2020 09:54:14: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:54:14: #2 You may need to consider one of the other alternative d(s): 2,49,563 WARNING @ Tue, 16 Jun 2020 09:54:14: #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 09:54:14: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:54:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:54:17: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:54:23: 10000000 INFO @ Tue, 16 Jun 2020 09:54:29: 11000000 INFO @ Tue, 16 Jun 2020 09:54:31: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:54:31: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:54:31: #1 total tags in treatment: 11391728 INFO @ Tue, 16 Jun 2020 09:54:31: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:54:31: #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 09:54:31: #1 tags after filtering in treatment: 11391728 INFO @ Tue, 16 Jun 2020 09:54:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:54:31: #1 finished! INFO @ Tue, 16 Jun 2020 09:54:31: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:54:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:54:32: #2 number of paired peaks: 271 WARNING @ Tue, 16 Jun 2020 09:54:32: Fewer paired peaks (271) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 271 pairs to build model! INFO @ Tue, 16 Jun 2020 09:54:32: start model_add_line... INFO @ Tue, 16 Jun 2020 09:54:32: start X-correlation... INFO @ Tue, 16 Jun 2020 09:54:32: end of X-cor INFO @ Tue, 16 Jun 2020 09:54:32: #2 finished! INFO @ Tue, 16 Jun 2020 09:54:32: #2 predicted fragment length is 49 bps INFO @ Tue, 16 Jun 2020 09:54:32: #2 alternative fragment length(s) may be 2,49,563 bps INFO @ Tue, 16 Jun 2020 09:54:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982096/SRX982096.20_model.r WARNING @ Tue, 16 Jun 2020 09:54:32: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:54:32: #2 You may need to consider one of the other alternative d(s): 2,49,563 WARNING @ Tue, 16 Jun 2020 09:54:32: #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 09:54:32: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:54:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:54:36: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:54:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982096/SRX982096.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:54:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982096/SRX982096.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:54:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982096/SRX982096.10_summits.bed INFO @ Tue, 16 Jun 2020 09:54:47: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (364 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:54:55: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:55:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982096/SRX982096.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:55:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982096/SRX982096.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:55:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982096/SRX982096.20_summits.bed INFO @ Tue, 16 Jun 2020 09:55:06: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (144 records, 4 fields): 1 millis CompletedMACS2peakCalling