Job ID = 6366944 SRX = SRX2576645 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:15:17 prefetch.2.10.7: 1) Downloading 'SRR5272602'... 2020-06-15T23:15:17 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:16:32 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:16:33 prefetch.2.10.7: 'SRR5272602' is valid 2020-06-15T23:16:33 prefetch.2.10.7: 1) 'SRR5272602' was downloaded successfully 2020-06-15T23:16:33 prefetch.2.10.7: 'SRR5272602' has 0 unresolved dependencies Read 19611087 spots for SRR5272602/SRR5272602.sra Written 19611087 spots for SRR5272602/SRR5272602.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: 00:04:13 19611087 reads; of these: 19611087 (100.00%) were unpaired; of these: 1907040 (9.72%) aligned 0 times 14449592 (73.68%) aligned exactly 1 time 3254455 (16.59%) aligned >1 times 90.28% overall alignment rate Time searching: 00:04:13 Overall time: 00:04:13 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] 8891300 / 17704047 = 0.5022 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 08:24:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576645/SRX2576645.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576645/SRX2576645.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576645/SRX2576645.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576645/SRX2576645.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 08:24:49: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:24:49: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:24:55: 1000000 INFO @ Tue, 16 Jun 2020 08:25:00: 2000000 INFO @ Tue, 16 Jun 2020 08:25:05: 3000000 INFO @ Tue, 16 Jun 2020 08:25:11: 4000000 INFO @ Tue, 16 Jun 2020 08:25:16: 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 @ Tue, 16 Jun 2020 08:25:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576645/SRX2576645.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576645/SRX2576645.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576645/SRX2576645.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576645/SRX2576645.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 08:25:19: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:25:19: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:25:21: 6000000 INFO @ Tue, 16 Jun 2020 08:25:25: 1000000 INFO @ Tue, 16 Jun 2020 08:25:27: 7000000 INFO @ Tue, 16 Jun 2020 08:25:31: 2000000 INFO @ Tue, 16 Jun 2020 08:25:32: 8000000 INFO @ Tue, 16 Jun 2020 08:25:36: 3000000 INFO @ Tue, 16 Jun 2020 08:25:37: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:25:37: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:25:37: #1 total tags in treatment: 8812747 INFO @ Tue, 16 Jun 2020 08:25:37: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:25:37: #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 08:25:37: #1 tags after filtering in treatment: 8812747 INFO @ Tue, 16 Jun 2020 08:25:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:25:37: #1 finished! INFO @ Tue, 16 Jun 2020 08:25:37: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:25:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:25:37: #2 number of paired peaks: 473 WARNING @ Tue, 16 Jun 2020 08:25:37: Fewer paired peaks (473) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 473 pairs to build model! INFO @ Tue, 16 Jun 2020 08:25:37: start model_add_line... INFO @ Tue, 16 Jun 2020 08:25:37: start X-correlation... INFO @ Tue, 16 Jun 2020 08:25:37: end of X-cor INFO @ Tue, 16 Jun 2020 08:25:37: #2 finished! INFO @ Tue, 16 Jun 2020 08:25:37: #2 predicted fragment length is 58 bps INFO @ Tue, 16 Jun 2020 08:25:37: #2 alternative fragment length(s) may be 4,58,581 bps INFO @ Tue, 16 Jun 2020 08:25:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576645/SRX2576645.05_model.r WARNING @ Tue, 16 Jun 2020 08:25:37: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:25:37: #2 You may need to consider one of the other alternative d(s): 4,58,581 WARNING @ Tue, 16 Jun 2020 08:25:37: #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 08:25:37: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:25:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:25:42: 4000000 INFO @ Tue, 16 Jun 2020 08:25:47: 5000000 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 08:25:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2576645/SRX2576645.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2576645/SRX2576645.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2576645/SRX2576645.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2576645/SRX2576645.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 08:25:49: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:25:49: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:25:53: 6000000 INFO @ Tue, 16 Jun 2020 08:25:55: 1000000 INFO @ Tue, 16 Jun 2020 08:25:56: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:25:58: 7000000 INFO @ Tue, 16 Jun 2020 08:26:00: 2000000 INFO @ Tue, 16 Jun 2020 08:26:04: 8000000 INFO @ Tue, 16 Jun 2020 08:26:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576645/SRX2576645.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:26:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576645/SRX2576645.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:26:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576645/SRX2576645.05_summits.bed INFO @ Tue, 16 Jun 2020 08:26:05: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1192 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:26:06: 3000000 INFO @ Tue, 16 Jun 2020 08:26:08: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:26:08: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:26:08: #1 total tags in treatment: 8812747 INFO @ Tue, 16 Jun 2020 08:26:08: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:26:08: #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 08:26:08: #1 tags after filtering in treatment: 8812747 INFO @ Tue, 16 Jun 2020 08:26:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:26:08: #1 finished! INFO @ Tue, 16 Jun 2020 08:26:08: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:26:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:26:09: #2 number of paired peaks: 473 WARNING @ Tue, 16 Jun 2020 08:26:09: Fewer paired peaks (473) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 473 pairs to build model! INFO @ Tue, 16 Jun 2020 08:26:09: start model_add_line... INFO @ Tue, 16 Jun 2020 08:26:09: start X-correlation... INFO @ Tue, 16 Jun 2020 08:26:09: end of X-cor INFO @ Tue, 16 Jun 2020 08:26:09: #2 finished! INFO @ Tue, 16 Jun 2020 08:26:09: #2 predicted fragment length is 58 bps INFO @ Tue, 16 Jun 2020 08:26:09: #2 alternative fragment length(s) may be 4,58,581 bps INFO @ Tue, 16 Jun 2020 08:26:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576645/SRX2576645.10_model.r WARNING @ Tue, 16 Jun 2020 08:26:09: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:26:09: #2 You may need to consider one of the other alternative d(s): 4,58,581 WARNING @ Tue, 16 Jun 2020 08:26:09: #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 08:26:09: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:26:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:26:11: 4000000 INFO @ Tue, 16 Jun 2020 08:26:17: 5000000 INFO @ Tue, 16 Jun 2020 08:26:22: 6000000 INFO @ Tue, 16 Jun 2020 08:26:27: 7000000 INFO @ Tue, 16 Jun 2020 08:26:28: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:26:32: 8000000 INFO @ Tue, 16 Jun 2020 08:26:36: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:26:36: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:26:36: #1 total tags in treatment: 8812747 INFO @ Tue, 16 Jun 2020 08:26:36: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:26:36: #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 08:26:37: #1 tags after filtering in treatment: 8812747 INFO @ Tue, 16 Jun 2020 08:26:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:26:37: #1 finished! INFO @ Tue, 16 Jun 2020 08:26:37: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:26:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:26:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576645/SRX2576645.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:26:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576645/SRX2576645.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:26:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576645/SRX2576645.10_summits.bed INFO @ Tue, 16 Jun 2020 08:26:37: Done! INFO @ Tue, 16 Jun 2020 08:26:37: #2 number of paired peaks: 473 WARNING @ Tue, 16 Jun 2020 08:26:37: Fewer paired peaks (473) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 473 pairs to build model! INFO @ Tue, 16 Jun 2020 08:26:37: start model_add_line... pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (747 records, 4 fields): 1 millis INFO @ Tue, 16 Jun 2020 08:26:37: start X-correlation... CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:26:37: end of X-cor INFO @ Tue, 16 Jun 2020 08:26:37: #2 finished! INFO @ Tue, 16 Jun 2020 08:26:37: #2 predicted fragment length is 58 bps INFO @ Tue, 16 Jun 2020 08:26:37: #2 alternative fragment length(s) may be 4,58,581 bps INFO @ Tue, 16 Jun 2020 08:26:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2576645/SRX2576645.20_model.r WARNING @ Tue, 16 Jun 2020 08:26:37: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:26:37: #2 You may need to consider one of the other alternative d(s): 4,58,581 WARNING @ Tue, 16 Jun 2020 08:26:37: #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 08:26:37: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:26:37: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:26:56: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:27:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2576645/SRX2576645.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:27:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2576645/SRX2576645.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:27:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2576645/SRX2576645.20_summits.bed INFO @ Tue, 16 Jun 2020 08:27:05: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (303 records, 4 fields): 2 millis CompletedMACS2peakCalling