Job ID = 6367168 SRX = SRX2965742 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:23:31 prefetch.2.10.7: 1) Downloading 'SRR5766327'... 2020-06-15T23:23:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:27:20 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:27:20 prefetch.2.10.7: 1) 'SRR5766327' was downloaded successfully Read 22743849 spots for SRR5766327/SRR5766327.sra Written 22743849 spots for SRR5766327/SRR5766327.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: 00:07:49 22743849 reads; of these: 22743849 (100.00%) were unpaired; of these: 9629966 (42.34%) aligned 0 times 11177556 (49.15%) aligned exactly 1 time 1936327 (8.51%) aligned >1 times 57.66% overall alignment rate Time searching: 00:07:49 Overall time: 00:07:49 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] 1849876 / 13113883 = 0.1411 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 08:41:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2965742/SRX2965742.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2965742/SRX2965742.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2965742/SRX2965742.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2965742/SRX2965742.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 08:41:32: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:41:32: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:41:42: 1000000 INFO @ Tue, 16 Jun 2020 08:41:52: 2000000 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 08:42:01: 3000000 INFO @ Tue, 16 Jun 2020 08:42:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2965742/SRX2965742.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2965742/SRX2965742.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2965742/SRX2965742.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2965742/SRX2965742.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 08:42:02: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:42:02: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:42:12: 4000000 INFO @ Tue, 16 Jun 2020 08:42:13: 1000000 INFO @ Tue, 16 Jun 2020 08:42:23: 5000000 INFO @ Tue, 16 Jun 2020 08:42:24: 2000000 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 08:42:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2965742/SRX2965742.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2965742/SRX2965742.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2965742/SRX2965742.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2965742/SRX2965742.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 08:42:32: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:42:32: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:42:34: 6000000 INFO @ Tue, 16 Jun 2020 08:42:35: 3000000 INFO @ Tue, 16 Jun 2020 08:42:43: 1000000 INFO @ Tue, 16 Jun 2020 08:42:45: 7000000 INFO @ Tue, 16 Jun 2020 08:42:47: 4000000 INFO @ Tue, 16 Jun 2020 08:42:55: 2000000 INFO @ Tue, 16 Jun 2020 08:42:56: 8000000 INFO @ Tue, 16 Jun 2020 08:42:58: 5000000 INFO @ Tue, 16 Jun 2020 08:43:05: 3000000 INFO @ Tue, 16 Jun 2020 08:43:07: 9000000 INFO @ Tue, 16 Jun 2020 08:43:09: 6000000 INFO @ Tue, 16 Jun 2020 08:43:16: 4000000 INFO @ Tue, 16 Jun 2020 08:43:19: 10000000 INFO @ Tue, 16 Jun 2020 08:43:20: 7000000 INFO @ Tue, 16 Jun 2020 08:43:26: 5000000 INFO @ Tue, 16 Jun 2020 08:43:30: 11000000 INFO @ Tue, 16 Jun 2020 08:43:31: 8000000 INFO @ Tue, 16 Jun 2020 08:43:33: #1 tag size is determined as 101 bps INFO @ Tue, 16 Jun 2020 08:43:33: #1 tag size = 101 INFO @ Tue, 16 Jun 2020 08:43:33: #1 total tags in treatment: 11264007 INFO @ Tue, 16 Jun 2020 08:43:33: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:43:33: #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 08:43:33: #1 tags after filtering in treatment: 11264007 INFO @ Tue, 16 Jun 2020 08:43:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:43:33: #1 finished! INFO @ Tue, 16 Jun 2020 08:43:33: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:43:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:43:34: #2 number of paired peaks: 862 WARNING @ Tue, 16 Jun 2020 08:43:34: Fewer paired peaks (862) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 862 pairs to build model! INFO @ Tue, 16 Jun 2020 08:43:34: start model_add_line... INFO @ Tue, 16 Jun 2020 08:43:34: start X-correlation... INFO @ Tue, 16 Jun 2020 08:43:34: end of X-cor INFO @ Tue, 16 Jun 2020 08:43:34: #2 finished! INFO @ Tue, 16 Jun 2020 08:43:34: #2 predicted fragment length is 146 bps INFO @ Tue, 16 Jun 2020 08:43:34: #2 alternative fragment length(s) may be 146 bps INFO @ Tue, 16 Jun 2020 08:43:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2965742/SRX2965742.05_model.r WARNING @ Tue, 16 Jun 2020 08:43:34: #2 Since the d (146) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:43:34: #2 You may need to consider one of the other alternative d(s): 146 WARNING @ Tue, 16 Jun 2020 08:43:34: #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 08:43:34: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:43:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:43:37: 6000000 INFO @ Tue, 16 Jun 2020 08:43:42: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:43:47: 7000000 INFO @ Tue, 16 Jun 2020 08:43:52: 10000000 INFO @ Tue, 16 Jun 2020 08:43:58: 8000000 INFO @ Tue, 16 Jun 2020 08:43:59: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:44:03: 11000000 INFO @ Tue, 16 Jun 2020 08:44:06: #1 tag size is determined as 101 bps INFO @ Tue, 16 Jun 2020 08:44:06: #1 tag size = 101 INFO @ Tue, 16 Jun 2020 08:44:06: #1 total tags in treatment: 11264007 INFO @ Tue, 16 Jun 2020 08:44:06: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:44:06: #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 08:44:06: #1 tags after filtering in treatment: 11264007 INFO @ Tue, 16 Jun 2020 08:44:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:44:06: #1 finished! INFO @ Tue, 16 Jun 2020 08:44:06: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:44:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:44:07: #2 number of paired peaks: 862 WARNING @ Tue, 16 Jun 2020 08:44:07: Fewer paired peaks (862) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 862 pairs to build model! INFO @ Tue, 16 Jun 2020 08:44:07: start model_add_line... INFO @ Tue, 16 Jun 2020 08:44:07: start X-correlation... INFO @ Tue, 16 Jun 2020 08:44:07: end of X-cor INFO @ Tue, 16 Jun 2020 08:44:07: #2 finished! INFO @ Tue, 16 Jun 2020 08:44:07: #2 predicted fragment length is 146 bps INFO @ Tue, 16 Jun 2020 08:44:07: #2 alternative fragment length(s) may be 146 bps INFO @ Tue, 16 Jun 2020 08:44:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2965742/SRX2965742.10_model.r WARNING @ Tue, 16 Jun 2020 08:44:07: #2 Since the d (146) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:44:07: #2 You may need to consider one of the other alternative d(s): 146 WARNING @ Tue, 16 Jun 2020 08:44:07: #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 08:44:07: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:44:07: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:44:08: 9000000 INFO @ Tue, 16 Jun 2020 08:44:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2965742/SRX2965742.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:44:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2965742/SRX2965742.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:44:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2965742/SRX2965742.05_summits.bed INFO @ Tue, 16 Jun 2020 08:44:13: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3870 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:44:18: 10000000 INFO @ Tue, 16 Jun 2020 08:44:27: 11000000 INFO @ Tue, 16 Jun 2020 08:44:30: #1 tag size is determined as 101 bps INFO @ Tue, 16 Jun 2020 08:44:30: #1 tag size = 101 INFO @ Tue, 16 Jun 2020 08:44:30: #1 total tags in treatment: 11264007 INFO @ Tue, 16 Jun 2020 08:44:30: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:44:30: #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 08:44:30: #1 tags after filtering in treatment: 11264007 INFO @ Tue, 16 Jun 2020 08:44:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:44:30: #1 finished! INFO @ Tue, 16 Jun 2020 08:44:30: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:44:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:44:31: #2 number of paired peaks: 862 WARNING @ Tue, 16 Jun 2020 08:44:31: Fewer paired peaks (862) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 862 pairs to build model! INFO @ Tue, 16 Jun 2020 08:44:31: start model_add_line... INFO @ Tue, 16 Jun 2020 08:44:31: start X-correlation... INFO @ Tue, 16 Jun 2020 08:44:31: end of X-cor INFO @ Tue, 16 Jun 2020 08:44:31: #2 finished! INFO @ Tue, 16 Jun 2020 08:44:31: #2 predicted fragment length is 146 bps INFO @ Tue, 16 Jun 2020 08:44:31: #2 alternative fragment length(s) may be 146 bps INFO @ Tue, 16 Jun 2020 08:44:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2965742/SRX2965742.20_model.r WARNING @ Tue, 16 Jun 2020 08:44:31: #2 Since the d (146) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:44:31: #2 You may need to consider one of the other alternative d(s): 146 WARNING @ Tue, 16 Jun 2020 08:44:31: #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 08:44:31: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:44:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:44:33: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:44:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2965742/SRX2965742.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:44:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2965742/SRX2965742.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:44:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2965742/SRX2965742.10_summits.bed INFO @ Tue, 16 Jun 2020 08:44:47: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2812 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:44:57: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:45:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2965742/SRX2965742.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:45:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2965742/SRX2965742.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:45:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2965742/SRX2965742.20_summits.bed INFO @ Tue, 16 Jun 2020 08:45:11: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1742 records, 4 fields): 3 millis CompletedMACS2peakCalling