Job ID = 6368631 SRX = SRX5073499 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:20:36 prefetch.2.10.7: 1) Downloading 'SRR8255719'... 2020-06-16T00:20:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:22:37 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:22:38 prefetch.2.10.7: 'SRR8255719' is valid 2020-06-16T00:22:38 prefetch.2.10.7: 1) 'SRR8255719' was downloaded successfully 2020-06-16T00:22:38 prefetch.2.10.7: 'SRR8255719' has 0 unresolved dependencies Read 27409706 spots for SRR8255719/SRR8255719.sra Written 27409706 spots for SRR8255719/SRR8255719.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: 00:05:53 27409706 reads; of these: 27409706 (100.00%) were unpaired; of these: 1825277 (6.66%) aligned 0 times 21332263 (77.83%) aligned exactly 1 time 4252166 (15.51%) aligned >1 times 93.34% overall alignment rate Time searching: 00:05:53 Overall time: 00:05:53 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] 7476151 / 25584429 = 0.2922 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 09:34:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5073499/SRX5073499.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5073499/SRX5073499.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5073499/SRX5073499.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5073499/SRX5073499.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 09:34:01: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:34:01: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:34:06: 1000000 INFO @ Tue, 16 Jun 2020 09:34:11: 2000000 INFO @ Tue, 16 Jun 2020 09:34:15: 3000000 INFO @ Tue, 16 Jun 2020 09:34:20: 4000000 INFO @ Tue, 16 Jun 2020 09:34:25: 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 09:34:30: 6000000 INFO @ Tue, 16 Jun 2020 09:34:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5073499/SRX5073499.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5073499/SRX5073499.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5073499/SRX5073499.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5073499/SRX5073499.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 09:34:31: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:34:31: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:34:36: 7000000 INFO @ Tue, 16 Jun 2020 09:34:37: 1000000 INFO @ Tue, 16 Jun 2020 09:34:42: 8000000 INFO @ Tue, 16 Jun 2020 09:34:43: 2000000 INFO @ Tue, 16 Jun 2020 09:34:47: 9000000 INFO @ Tue, 16 Jun 2020 09:34:49: 3000000 INFO @ Tue, 16 Jun 2020 09:34:53: 10000000 INFO @ Tue, 16 Jun 2020 09:34:56: 4000000 INFO @ Tue, 16 Jun 2020 09:34:59: 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 @ Tue, 16 Jun 2020 09:35:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5073499/SRX5073499.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5073499/SRX5073499.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5073499/SRX5073499.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5073499/SRX5073499.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 09:35:01: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:35:01: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:35:02: 5000000 INFO @ Tue, 16 Jun 2020 09:35:05: 12000000 INFO @ Tue, 16 Jun 2020 09:35:07: 1000000 INFO @ Tue, 16 Jun 2020 09:35:08: 6000000 INFO @ Tue, 16 Jun 2020 09:35:10: 13000000 INFO @ Tue, 16 Jun 2020 09:35:12: 2000000 INFO @ Tue, 16 Jun 2020 09:35:15: 7000000 INFO @ Tue, 16 Jun 2020 09:35:16: 14000000 INFO @ Tue, 16 Jun 2020 09:35:18: 3000000 INFO @ Tue, 16 Jun 2020 09:35:21: 8000000 INFO @ Tue, 16 Jun 2020 09:35:22: 15000000 INFO @ Tue, 16 Jun 2020 09:35:23: 4000000 INFO @ Tue, 16 Jun 2020 09:35:27: 9000000 INFO @ Tue, 16 Jun 2020 09:35:27: 16000000 INFO @ Tue, 16 Jun 2020 09:35:29: 5000000 INFO @ Tue, 16 Jun 2020 09:35:33: 17000000 INFO @ Tue, 16 Jun 2020 09:35:34: 10000000 INFO @ Tue, 16 Jun 2020 09:35:35: 6000000 INFO @ Tue, 16 Jun 2020 09:35:38: 18000000 INFO @ Tue, 16 Jun 2020 09:35:39: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:35:39: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:35:39: #1 total tags in treatment: 18108278 INFO @ Tue, 16 Jun 2020 09:35:39: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:35:39: #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 09:35:39: #1 tags after filtering in treatment: 18108278 INFO @ Tue, 16 Jun 2020 09:35:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:35:39: #1 finished! INFO @ Tue, 16 Jun 2020 09:35:39: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:35:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:35:40: 11000000 INFO @ Tue, 16 Jun 2020 09:35:40: 7000000 INFO @ Tue, 16 Jun 2020 09:35:40: #2 number of paired peaks: 163 WARNING @ Tue, 16 Jun 2020 09:35:40: Fewer paired peaks (163) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 163 pairs to build model! INFO @ Tue, 16 Jun 2020 09:35:40: start model_add_line... INFO @ Tue, 16 Jun 2020 09:35:41: start X-correlation... INFO @ Tue, 16 Jun 2020 09:35:41: end of X-cor INFO @ Tue, 16 Jun 2020 09:35:41: #2 finished! INFO @ Tue, 16 Jun 2020 09:35:41: #2 predicted fragment length is 47 bps INFO @ Tue, 16 Jun 2020 09:35:41: #2 alternative fragment length(s) may be 1,47,109,551,571,574,582 bps INFO @ Tue, 16 Jun 2020 09:35:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5073499/SRX5073499.05_model.r WARNING @ Tue, 16 Jun 2020 09:35:41: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:35:41: #2 You may need to consider one of the other alternative d(s): 1,47,109,551,571,574,582 WARNING @ Tue, 16 Jun 2020 09:35:41: #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 09:35:41: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:35:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:35:46: 8000000 INFO @ Tue, 16 Jun 2020 09:35:46: 12000000 INFO @ Tue, 16 Jun 2020 09:35:51: 9000000 INFO @ Tue, 16 Jun 2020 09:35:52: 13000000 INFO @ Tue, 16 Jun 2020 09:35:57: 10000000 INFO @ Tue, 16 Jun 2020 09:35:58: 14000000 INFO @ Tue, 16 Jun 2020 09:36:02: 11000000 INFO @ Tue, 16 Jun 2020 09:36:05: 15000000 INFO @ Tue, 16 Jun 2020 09:36:08: 12000000 INFO @ Tue, 16 Jun 2020 09:36:10: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:36:11: 16000000 INFO @ Tue, 16 Jun 2020 09:36:13: 13000000 INFO @ Tue, 16 Jun 2020 09:36:17: 17000000 INFO @ Tue, 16 Jun 2020 09:36:19: 14000000 INFO @ Tue, 16 Jun 2020 09:36:23: 18000000 INFO @ Tue, 16 Jun 2020 09:36:24: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:36:24: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:36:24: #1 total tags in treatment: 18108278 INFO @ Tue, 16 Jun 2020 09:36:24: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:36:24: #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 09:36:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5073499/SRX5073499.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:36:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5073499/SRX5073499.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:36:24: #1 tags after filtering in treatment: 18108278 INFO @ Tue, 16 Jun 2020 09:36:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5073499/SRX5073499.05_summits.bed INFO @ Tue, 16 Jun 2020 09:36:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:36:24: #1 finished! INFO @ Tue, 16 Jun 2020 09:36:24: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:36:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:36:24: Done! INFO @ Tue, 16 Jun 2020 09:36:24: 15000000 pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1044 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:36:25: #2 number of paired peaks: 163 WARNING @ Tue, 16 Jun 2020 09:36:25: Fewer paired peaks (163) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 163 pairs to build model! INFO @ Tue, 16 Jun 2020 09:36:25: start model_add_line... INFO @ Tue, 16 Jun 2020 09:36:25: start X-correlation... INFO @ Tue, 16 Jun 2020 09:36:25: end of X-cor INFO @ Tue, 16 Jun 2020 09:36:25: #2 finished! INFO @ Tue, 16 Jun 2020 09:36:25: #2 predicted fragment length is 47 bps INFO @ Tue, 16 Jun 2020 09:36:25: #2 alternative fragment length(s) may be 1,47,109,551,571,574,582 bps INFO @ Tue, 16 Jun 2020 09:36:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5073499/SRX5073499.10_model.r WARNING @ Tue, 16 Jun 2020 09:36:25: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:36:25: #2 You may need to consider one of the other alternative d(s): 1,47,109,551,571,574,582 WARNING @ Tue, 16 Jun 2020 09:36:25: #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 09:36:25: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:36:25: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:36:29: 16000000 INFO @ Tue, 16 Jun 2020 09:36:34: 17000000 INFO @ Tue, 16 Jun 2020 09:36:40: 18000000 INFO @ Tue, 16 Jun 2020 09:36:40: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:36:40: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:36:40: #1 total tags in treatment: 18108278 INFO @ Tue, 16 Jun 2020 09:36:40: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:36:40: #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 09:36:40: #1 tags after filtering in treatment: 18108278 INFO @ Tue, 16 Jun 2020 09:36:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:36:40: #1 finished! INFO @ Tue, 16 Jun 2020 09:36:40: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:36:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:36:42: #2 number of paired peaks: 163 WARNING @ Tue, 16 Jun 2020 09:36:42: Fewer paired peaks (163) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 163 pairs to build model! INFO @ Tue, 16 Jun 2020 09:36:42: start model_add_line... INFO @ Tue, 16 Jun 2020 09:36:42: start X-correlation... INFO @ Tue, 16 Jun 2020 09:36:42: end of X-cor INFO @ Tue, 16 Jun 2020 09:36:42: #2 finished! INFO @ Tue, 16 Jun 2020 09:36:42: #2 predicted fragment length is 47 bps INFO @ Tue, 16 Jun 2020 09:36:42: #2 alternative fragment length(s) may be 1,47,109,551,571,574,582 bps INFO @ Tue, 16 Jun 2020 09:36:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5073499/SRX5073499.20_model.r WARNING @ Tue, 16 Jun 2020 09:36:42: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:36:42: #2 You may need to consider one of the other alternative d(s): 1,47,109,551,571,574,582 WARNING @ Tue, 16 Jun 2020 09:36:42: #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 09:36:42: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:36:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:36:55: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:37:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5073499/SRX5073499.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:37:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5073499/SRX5073499.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:37:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5073499/SRX5073499.10_summits.bed INFO @ Tue, 16 Jun 2020 09:37:09: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (422 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:37:11: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:37:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5073499/SRX5073499.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:37:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5073499/SRX5073499.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:37:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5073499/SRX5073499.20_summits.bed INFO @ Tue, 16 Jun 2020 09:37:25: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (137 records, 4 fields): 1 millis CompletedMACS2peakCalling