Job ID = 6507964 SRX = SRX495122 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T12:58:11 prefetch.2.10.7: 1) Downloading 'SRR1198654'... 2020-06-26T12:58:11 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:00:07 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:00:07 prefetch.2.10.7: 1) 'SRR1198654' was downloaded successfully Read 22015477 spots for SRR1198654/SRR1198654.sra Written 22015477 spots for SRR1198654/SRR1198654.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: 00:04:40 22015477 reads; of these: 22015477 (100.00%) were unpaired; of these: 1904080 (8.65%) aligned 0 times 16767927 (76.16%) aligned exactly 1 time 3343470 (15.19%) aligned >1 times 91.35% overall alignment rate Time searching: 00:04:41 Overall time: 00:04:41 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] 5878208 / 20111397 = 0.2923 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 @ Fri, 26 Jun 2020 22:10:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495122/SRX495122.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495122/SRX495122.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495122/SRX495122.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495122/SRX495122.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 @ Fri, 26 Jun 2020 22:10:44: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:10:44: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:10:50: 1000000 INFO @ Fri, 26 Jun 2020 22:10:55: 2000000 INFO @ Fri, 26 Jun 2020 22:11:00: 3000000 INFO @ Fri, 26 Jun 2020 22:11:06: 4000000 INFO @ Fri, 26 Jun 2020 22:11:11: 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 @ Fri, 26 Jun 2020 22:11:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495122/SRX495122.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495122/SRX495122.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495122/SRX495122.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495122/SRX495122.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 @ Fri, 26 Jun 2020 22:11:14: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:11:14: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:11:16: 6000000 INFO @ Fri, 26 Jun 2020 22:11:21: 1000000 INFO @ Fri, 26 Jun 2020 22:11:22: 7000000 INFO @ Fri, 26 Jun 2020 22:11:27: 2000000 INFO @ Fri, 26 Jun 2020 22:11:28: 8000000 INFO @ Fri, 26 Jun 2020 22:11:33: 3000000 INFO @ Fri, 26 Jun 2020 22:11:34: 9000000 INFO @ Fri, 26 Jun 2020 22:11:40: 10000000 INFO @ Fri, 26 Jun 2020 22:11:40: 4000000 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 @ Fri, 26 Jun 2020 22:11:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX495122/SRX495122.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX495122/SRX495122.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX495122/SRX495122.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX495122/SRX495122.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 @ Fri, 26 Jun 2020 22:11:44: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:11:44: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:11:45: 11000000 INFO @ Fri, 26 Jun 2020 22:11:46: 5000000 INFO @ Fri, 26 Jun 2020 22:11:50: 1000000 INFO @ Fri, 26 Jun 2020 22:11:51: 12000000 INFO @ Fri, 26 Jun 2020 22:11:52: 6000000 INFO @ Fri, 26 Jun 2020 22:11:56: 2000000 INFO @ Fri, 26 Jun 2020 22:11:57: 13000000 INFO @ Fri, 26 Jun 2020 22:11:59: 7000000 INFO @ Fri, 26 Jun 2020 22:12:02: 3000000 INFO @ Fri, 26 Jun 2020 22:12:03: 14000000 INFO @ Fri, 26 Jun 2020 22:12:05: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 22:12:05: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 22:12:05: #1 total tags in treatment: 14233189 INFO @ Fri, 26 Jun 2020 22:12:05: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:12:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:12:05: #1 tags after filtering in treatment: 14233189 INFO @ Fri, 26 Jun 2020 22:12:05: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:12:05: #1 finished! INFO @ Fri, 26 Jun 2020 22:12:05: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:12:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:12:05: 8000000 INFO @ Fri, 26 Jun 2020 22:12:06: #2 number of paired peaks: 272 WARNING @ Fri, 26 Jun 2020 22:12:06: Fewer paired peaks (272) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 272 pairs to build model! INFO @ Fri, 26 Jun 2020 22:12:06: start model_add_line... INFO @ Fri, 26 Jun 2020 22:12:06: start X-correlation... INFO @ Fri, 26 Jun 2020 22:12:06: end of X-cor INFO @ Fri, 26 Jun 2020 22:12:06: #2 finished! INFO @ Fri, 26 Jun 2020 22:12:06: #2 predicted fragment length is 44 bps INFO @ Fri, 26 Jun 2020 22:12:06: #2 alternative fragment length(s) may be 2,44 bps INFO @ Fri, 26 Jun 2020 22:12:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495122/SRX495122.05_model.r WARNING @ Fri, 26 Jun 2020 22:12:06: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:12:06: #2 You may need to consider one of the other alternative d(s): 2,44 WARNING @ Fri, 26 Jun 2020 22:12:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:12:06: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:12:06: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:12:08: 4000000 INFO @ Fri, 26 Jun 2020 22:12:11: 9000000 INFO @ Fri, 26 Jun 2020 22:12:14: 5000000 INFO @ Fri, 26 Jun 2020 22:12:18: 10000000 INFO @ Fri, 26 Jun 2020 22:12:19: 6000000 INFO @ Fri, 26 Jun 2020 22:12:24: 11000000 INFO @ Fri, 26 Jun 2020 22:12:25: 7000000 INFO @ Fri, 26 Jun 2020 22:12:30: 12000000 INFO @ Fri, 26 Jun 2020 22:12:31: 8000000 INFO @ Fri, 26 Jun 2020 22:12:34: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:12:36: 9000000 INFO @ Fri, 26 Jun 2020 22:12:36: 13000000 INFO @ Fri, 26 Jun 2020 22:12:42: 10000000 INFO @ Fri, 26 Jun 2020 22:12:43: 14000000 INFO @ Fri, 26 Jun 2020 22:12:44: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 22:12:44: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 22:12:44: #1 total tags in treatment: 14233189 INFO @ Fri, 26 Jun 2020 22:12:44: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:12:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:12:45: #1 tags after filtering in treatment: 14233189 INFO @ Fri, 26 Jun 2020 22:12:45: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:12:45: #1 finished! INFO @ Fri, 26 Jun 2020 22:12:45: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:12:45: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:12:46: #2 number of paired peaks: 272 WARNING @ Fri, 26 Jun 2020 22:12:46: Fewer paired peaks (272) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 272 pairs to build model! INFO @ Fri, 26 Jun 2020 22:12:46: start model_add_line... INFO @ Fri, 26 Jun 2020 22:12:46: start X-correlation... INFO @ Fri, 26 Jun 2020 22:12:46: end of X-cor INFO @ Fri, 26 Jun 2020 22:12:46: #2 finished! INFO @ Fri, 26 Jun 2020 22:12:46: #2 predicted fragment length is 44 bps INFO @ Fri, 26 Jun 2020 22:12:46: #2 alternative fragment length(s) may be 2,44 bps INFO @ Fri, 26 Jun 2020 22:12:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495122/SRX495122.10_model.r WARNING @ Fri, 26 Jun 2020 22:12:46: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:12:46: #2 You may need to consider one of the other alternative d(s): 2,44 WARNING @ Fri, 26 Jun 2020 22:12:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:12:46: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:12:46: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:12:48: 11000000 INFO @ Fri, 26 Jun 2020 22:12:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495122/SRX495122.05_peaks.xls INFO @ Fri, 26 Jun 2020 22:12:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495122/SRX495122.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:12:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495122/SRX495122.05_summits.bed INFO @ Fri, 26 Jun 2020 22:12:48: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (736 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:12:53: 12000000 INFO @ Fri, 26 Jun 2020 22:12:58: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:13:03: 14000000 INFO @ Fri, 26 Jun 2020 22:13:05: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 22:13:05: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 22:13:05: #1 total tags in treatment: 14233189 INFO @ Fri, 26 Jun 2020 22:13:05: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:13:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:13:05: #1 tags after filtering in treatment: 14233189 INFO @ Fri, 26 Jun 2020 22:13:05: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 22:13:05: #1 finished! INFO @ Fri, 26 Jun 2020 22:13:05: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:13:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:13:06: #2 number of paired peaks: 272 WARNING @ Fri, 26 Jun 2020 22:13:06: Fewer paired peaks (272) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 272 pairs to build model! INFO @ Fri, 26 Jun 2020 22:13:06: start model_add_line... INFO @ Fri, 26 Jun 2020 22:13:06: start X-correlation... INFO @ Fri, 26 Jun 2020 22:13:06: end of X-cor INFO @ Fri, 26 Jun 2020 22:13:06: #2 finished! INFO @ Fri, 26 Jun 2020 22:13:06: #2 predicted fragment length is 44 bps INFO @ Fri, 26 Jun 2020 22:13:06: #2 alternative fragment length(s) may be 2,44 bps INFO @ Fri, 26 Jun 2020 22:13:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX495122/SRX495122.20_model.r WARNING @ Fri, 26 Jun 2020 22:13:06: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 22:13:06: #2 You may need to consider one of the other alternative d(s): 2,44 WARNING @ Fri, 26 Jun 2020 22:13:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 22:13:06: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:13:06: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:13:14: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:13:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495122/SRX495122.10_peaks.xls INFO @ Fri, 26 Jun 2020 22:13:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495122/SRX495122.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:13:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495122/SRX495122.10_summits.bed INFO @ Fri, 26 Jun 2020 22:13:29: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (448 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 22:13:34: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:13:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX495122/SRX495122.20_peaks.xls INFO @ Fri, 26 Jun 2020 22:13:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX495122/SRX495122.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:13:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX495122/SRX495122.20_summits.bed INFO @ Fri, 26 Jun 2020 22:13:48: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (177 records, 4 fields): 1 millis CompletedMACS2peakCalling