Job ID = 6369007 SRX = SRX982073 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:44:12 prefetch.2.10.7: 1) Downloading 'SRR1956552'... 2020-06-16T00:44:12 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:46:46 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:46:47 prefetch.2.10.7: 'SRR1956552' is valid 2020-06-16T00:46:47 prefetch.2.10.7: 1) 'SRR1956552' was downloaded successfully Read 14661660 spots for SRR1956552/SRR1956552.sra Written 14661660 spots for SRR1956552/SRR1956552.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: 00:03:27 14661660 reads; of these: 14661660 (100.00%) were unpaired; of these: 322800 (2.20%) aligned 0 times 11234541 (76.63%) aligned exactly 1 time 3104319 (21.17%) aligned >1 times 97.80% overall alignment rate Time searching: 00:03:27 Overall time: 00:03:27 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] 2044308 / 14338860 = 0.1426 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 09:55:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982073/SRX982073.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982073/SRX982073.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982073/SRX982073.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982073/SRX982073.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 09:55:13: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:55:13: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:55:19: 1000000 INFO @ Tue, 16 Jun 2020 09:55:24: 2000000 INFO @ Tue, 16 Jun 2020 09:55:30: 3000000 INFO @ Tue, 16 Jun 2020 09:55:35: 4000000 INFO @ Tue, 16 Jun 2020 09:55:41: 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 09:55:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982073/SRX982073.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982073/SRX982073.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982073/SRX982073.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982073/SRX982073.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 09:55:43: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:55:43: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:55:47: 6000000 INFO @ Tue, 16 Jun 2020 09:55:49: 1000000 INFO @ Tue, 16 Jun 2020 09:55:52: 7000000 INFO @ Tue, 16 Jun 2020 09:55:55: 2000000 INFO @ Tue, 16 Jun 2020 09:55:58: 8000000 INFO @ Tue, 16 Jun 2020 09:56:01: 3000000 INFO @ Tue, 16 Jun 2020 09:56:04: 9000000 INFO @ Tue, 16 Jun 2020 09:56:07: 4000000 INFO @ Tue, 16 Jun 2020 09:56:10: 10000000 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 09:56:13: 5000000 INFO @ Tue, 16 Jun 2020 09:56:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX982073/SRX982073.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX982073/SRX982073.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX982073/SRX982073.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX982073/SRX982073.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 09:56:13: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:56:13: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:56:15: 11000000 INFO @ Tue, 16 Jun 2020 09:56:19: 6000000 INFO @ Tue, 16 Jun 2020 09:56:19: 1000000 INFO @ Tue, 16 Jun 2020 09:56:21: 12000000 INFO @ Tue, 16 Jun 2020 09:56:23: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:56:23: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:56:23: #1 total tags in treatment: 12294552 INFO @ Tue, 16 Jun 2020 09:56:23: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:56:23: #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 09:56:23: #1 tags after filtering in treatment: 12294552 INFO @ Tue, 16 Jun 2020 09:56:23: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:56:23: #1 finished! INFO @ Tue, 16 Jun 2020 09:56:23: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:56:23: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:56:24: #2 number of paired peaks: 481 WARNING @ Tue, 16 Jun 2020 09:56:24: Fewer paired peaks (481) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 481 pairs to build model! INFO @ Tue, 16 Jun 2020 09:56:24: start model_add_line... INFO @ Tue, 16 Jun 2020 09:56:24: start X-correlation... INFO @ Tue, 16 Jun 2020 09:56:24: end of X-cor INFO @ Tue, 16 Jun 2020 09:56:24: #2 finished! INFO @ Tue, 16 Jun 2020 09:56:24: #2 predicted fragment length is 57 bps INFO @ Tue, 16 Jun 2020 09:56:24: #2 alternative fragment length(s) may be 3,57 bps INFO @ Tue, 16 Jun 2020 09:56:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982073/SRX982073.05_model.r WARNING @ Tue, 16 Jun 2020 09:56:24: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:56:24: #2 You may need to consider one of the other alternative d(s): 3,57 WARNING @ Tue, 16 Jun 2020 09:56:24: #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 09:56:24: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:56:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:56:25: 2000000 INFO @ Tue, 16 Jun 2020 09:56:25: 7000000 INFO @ Tue, 16 Jun 2020 09:56:30: 3000000 INFO @ Tue, 16 Jun 2020 09:56:31: 8000000 INFO @ Tue, 16 Jun 2020 09:56:36: 4000000 INFO @ Tue, 16 Jun 2020 09:56:37: 9000000 INFO @ Tue, 16 Jun 2020 09:56:41: 5000000 INFO @ Tue, 16 Jun 2020 09:56:43: 10000000 INFO @ Tue, 16 Jun 2020 09:56:47: 6000000 INFO @ Tue, 16 Jun 2020 09:56:48: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:56:49: 11000000 INFO @ Tue, 16 Jun 2020 09:56:52: 7000000 INFO @ Tue, 16 Jun 2020 09:56:55: 12000000 INFO @ Tue, 16 Jun 2020 09:56:57: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:56:57: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:56:57: #1 total tags in treatment: 12294552 INFO @ Tue, 16 Jun 2020 09:56:57: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:56:57: #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 09:56:57: #1 tags after filtering in treatment: 12294552 INFO @ Tue, 16 Jun 2020 09:56:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:56:57: #1 finished! INFO @ Tue, 16 Jun 2020 09:56:57: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:56:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:56:58: 8000000 INFO @ Tue, 16 Jun 2020 09:56:58: #2 number of paired peaks: 481 WARNING @ Tue, 16 Jun 2020 09:56:58: Fewer paired peaks (481) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 481 pairs to build model! INFO @ Tue, 16 Jun 2020 09:56:58: start model_add_line... INFO @ Tue, 16 Jun 2020 09:56:58: start X-correlation... INFO @ Tue, 16 Jun 2020 09:56:58: end of X-cor INFO @ Tue, 16 Jun 2020 09:56:58: #2 finished! INFO @ Tue, 16 Jun 2020 09:56:58: #2 predicted fragment length is 57 bps INFO @ Tue, 16 Jun 2020 09:56:58: #2 alternative fragment length(s) may be 3,57 bps INFO @ Tue, 16 Jun 2020 09:56:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982073/SRX982073.10_model.r WARNING @ Tue, 16 Jun 2020 09:56:58: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:56:58: #2 You may need to consider one of the other alternative d(s): 3,57 WARNING @ Tue, 16 Jun 2020 09:56:58: #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 09:56:58: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:56:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:57:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982073/SRX982073.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:57:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982073/SRX982073.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:57:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982073/SRX982073.05_summits.bed INFO @ Tue, 16 Jun 2020 09:57:01: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1896 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:57:03: 9000000 INFO @ Tue, 16 Jun 2020 09:57:09: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:57:14: 11000000 INFO @ Tue, 16 Jun 2020 09:57:19: 12000000 INFO @ Tue, 16 Jun 2020 09:57:21: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:57:21: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:57:21: #1 total tags in treatment: 12294552 INFO @ Tue, 16 Jun 2020 09:57:21: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:57:21: #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 09:57:21: #1 tags after filtering in treatment: 12294552 INFO @ Tue, 16 Jun 2020 09:57:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:57:21: #1 finished! INFO @ Tue, 16 Jun 2020 09:57:21: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:57:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:57:22: #2 number of paired peaks: 481 WARNING @ Tue, 16 Jun 2020 09:57:22: Fewer paired peaks (481) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 481 pairs to build model! INFO @ Tue, 16 Jun 2020 09:57:22: start model_add_line... INFO @ Tue, 16 Jun 2020 09:57:22: start X-correlation... INFO @ Tue, 16 Jun 2020 09:57:22: end of X-cor INFO @ Tue, 16 Jun 2020 09:57:22: #2 finished! INFO @ Tue, 16 Jun 2020 09:57:22: #2 predicted fragment length is 57 bps INFO @ Tue, 16 Jun 2020 09:57:22: #2 alternative fragment length(s) may be 3,57 bps INFO @ Tue, 16 Jun 2020 09:57:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX982073/SRX982073.20_model.r WARNING @ Tue, 16 Jun 2020 09:57:22: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:57:22: #2 You may need to consider one of the other alternative d(s): 3,57 WARNING @ Tue, 16 Jun 2020 09:57:22: #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 09:57:22: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:57:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:57:23: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:57:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982073/SRX982073.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:57:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982073/SRX982073.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:57:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982073/SRX982073.10_summits.bed INFO @ Tue, 16 Jun 2020 09:57:35: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (647 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:57:46: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:58:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX982073/SRX982073.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:58:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX982073/SRX982073.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:58:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX982073/SRX982073.20_summits.bed INFO @ Tue, 16 Jun 2020 09:58:00: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (219 records, 4 fields): 1 millis CompletedMACS2peakCalling