Job ID = 6366995 SRX = SRX257694 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:09:16 prefetch.2.10.7: 1) Downloading 'SRR800711'... 2020-06-15T23:09:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:11:06 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:11:07 prefetch.2.10.7: 'SRR800711' is valid 2020-06-15T23:11:07 prefetch.2.10.7: 1) 'SRR800711' was downloaded successfully Read 18854814 spots for SRR800711/SRR800711.sra Written 18854814 spots for SRR800711/SRR800711.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: 00:03:46 18854814 reads; of these: 18854814 (100.00%) were unpaired; of these: 288211 (1.53%) aligned 0 times 14954477 (79.31%) aligned exactly 1 time 3612126 (19.16%) aligned >1 times 98.47% overall alignment rate Time searching: 00:03:46 Overall time: 00:03:46 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] 3521900 / 18566603 = 0.1897 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 08:19:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257694/SRX257694.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257694/SRX257694.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257694/SRX257694.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257694/SRX257694.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 08:19:43: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:19:43: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:19:48: 1000000 INFO @ Tue, 16 Jun 2020 08:19:52: 2000000 INFO @ Tue, 16 Jun 2020 08:19:57: 3000000 INFO @ Tue, 16 Jun 2020 08:20:01: 4000000 INFO @ Tue, 16 Jun 2020 08:20:06: 5000000 INFO @ Tue, 16 Jun 2020 08:20:10: 6000000 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 08:20:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257694/SRX257694.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257694/SRX257694.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257694/SRX257694.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257694/SRX257694.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 08:20:13: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:20:13: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:20:15: 7000000 INFO @ Tue, 16 Jun 2020 08:20:18: 1000000 INFO @ Tue, 16 Jun 2020 08:20:19: 8000000 INFO @ Tue, 16 Jun 2020 08:20:22: 2000000 INFO @ Tue, 16 Jun 2020 08:20:24: 9000000 INFO @ Tue, 16 Jun 2020 08:20:27: 3000000 INFO @ Tue, 16 Jun 2020 08:20:29: 10000000 INFO @ Tue, 16 Jun 2020 08:20:31: 4000000 INFO @ Tue, 16 Jun 2020 08:20:33: 11000000 INFO @ Tue, 16 Jun 2020 08:20:36: 5000000 INFO @ Tue, 16 Jun 2020 08:20:38: 12000000 INFO @ Tue, 16 Jun 2020 08:20:41: 6000000 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 08:20:43: 13000000 INFO @ Tue, 16 Jun 2020 08:20:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX257694/SRX257694.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX257694/SRX257694.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX257694/SRX257694.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX257694/SRX257694.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 08:20:43: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:20:43: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:20:46: 7000000 INFO @ Tue, 16 Jun 2020 08:20:47: 14000000 INFO @ Tue, 16 Jun 2020 08:20:48: 1000000 INFO @ Tue, 16 Jun 2020 08:20:50: 8000000 INFO @ Tue, 16 Jun 2020 08:20:52: 15000000 INFO @ Tue, 16 Jun 2020 08:20:52: 2000000 INFO @ Tue, 16 Jun 2020 08:20:52: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 08:20:52: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 08:20:52: #1 total tags in treatment: 15044703 INFO @ Tue, 16 Jun 2020 08:20:52: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:20:52: #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 08:20:53: #1 tags after filtering in treatment: 15044703 INFO @ Tue, 16 Jun 2020 08:20:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:20:53: #1 finished! INFO @ Tue, 16 Jun 2020 08:20:53: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:20:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:20:54: #2 number of paired peaks: 416 WARNING @ Tue, 16 Jun 2020 08:20:54: Fewer paired peaks (416) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 416 pairs to build model! INFO @ Tue, 16 Jun 2020 08:20:54: start model_add_line... INFO @ Tue, 16 Jun 2020 08:20:54: start X-correlation... INFO @ Tue, 16 Jun 2020 08:20:54: end of X-cor INFO @ Tue, 16 Jun 2020 08:20:54: #2 finished! INFO @ Tue, 16 Jun 2020 08:20:54: #2 predicted fragment length is 57 bps INFO @ Tue, 16 Jun 2020 08:20:54: #2 alternative fragment length(s) may be 2,57 bps INFO @ Tue, 16 Jun 2020 08:20:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257694/SRX257694.05_model.r WARNING @ Tue, 16 Jun 2020 08:20:54: #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 08:20:54: #2 You may need to consider one of the other alternative d(s): 2,57 WARNING @ Tue, 16 Jun 2020 08:20:54: #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 08:20:54: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:20:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:20:55: 9000000 INFO @ Tue, 16 Jun 2020 08:20:57: 3000000 INFO @ Tue, 16 Jun 2020 08:21:00: 10000000 INFO @ Tue, 16 Jun 2020 08:21:02: 4000000 INFO @ Tue, 16 Jun 2020 08:21:05: 11000000 INFO @ Tue, 16 Jun 2020 08:21:06: 5000000 INFO @ Tue, 16 Jun 2020 08:21:10: 12000000 INFO @ Tue, 16 Jun 2020 08:21:11: 6000000 INFO @ Tue, 16 Jun 2020 08:21:14: 13000000 INFO @ Tue, 16 Jun 2020 08:21:15: 7000000 INFO @ Tue, 16 Jun 2020 08:21:19: 14000000 INFO @ Tue, 16 Jun 2020 08:21:20: 8000000 INFO @ Tue, 16 Jun 2020 08:21:21: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:21:24: 15000000 INFO @ Tue, 16 Jun 2020 08:21:24: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 08:21:24: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 08:21:24: #1 total tags in treatment: 15044703 INFO @ Tue, 16 Jun 2020 08:21:24: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:21:24: #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 08:21:24: #1 tags after filtering in treatment: 15044703 INFO @ Tue, 16 Jun 2020 08:21:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:21:24: #1 finished! INFO @ Tue, 16 Jun 2020 08:21:24: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:21:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:21:25: 9000000 INFO @ Tue, 16 Jun 2020 08:21:25: #2 number of paired peaks: 416 WARNING @ Tue, 16 Jun 2020 08:21:25: Fewer paired peaks (416) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 416 pairs to build model! INFO @ Tue, 16 Jun 2020 08:21:25: start model_add_line... INFO @ Tue, 16 Jun 2020 08:21:25: start X-correlation... INFO @ Tue, 16 Jun 2020 08:21:25: end of X-cor INFO @ Tue, 16 Jun 2020 08:21:25: #2 finished! INFO @ Tue, 16 Jun 2020 08:21:25: #2 predicted fragment length is 57 bps INFO @ Tue, 16 Jun 2020 08:21:25: #2 alternative fragment length(s) may be 2,57 bps INFO @ Tue, 16 Jun 2020 08:21:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257694/SRX257694.10_model.r WARNING @ Tue, 16 Jun 2020 08:21:25: #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 08:21:25: #2 You may need to consider one of the other alternative d(s): 2,57 WARNING @ Tue, 16 Jun 2020 08:21:25: #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 08:21:25: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:21:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:21:29: 10000000 INFO @ Tue, 16 Jun 2020 08:21:34: 11000000 INFO @ Tue, 16 Jun 2020 08:21:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257694/SRX257694.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:21:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257694/SRX257694.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:21:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257694/SRX257694.05_summits.bed INFO @ Tue, 16 Jun 2020 08:21:35: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5653 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:21:39: 12000000 INFO @ Tue, 16 Jun 2020 08:21:43: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:21:48: 14000000 INFO @ Tue, 16 Jun 2020 08:21:52: 15000000 INFO @ Tue, 16 Jun 2020 08:21:52: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 08:21:52: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 08:21:52: #1 total tags in treatment: 15044703 INFO @ Tue, 16 Jun 2020 08:21:52: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:21:52: #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 08:21:53: #1 tags after filtering in treatment: 15044703 INFO @ Tue, 16 Jun 2020 08:21:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:21:53: #1 finished! INFO @ Tue, 16 Jun 2020 08:21:53: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:21:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:21:53: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:21:54: #2 number of paired peaks: 416 WARNING @ Tue, 16 Jun 2020 08:21:54: Fewer paired peaks (416) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 416 pairs to build model! INFO @ Tue, 16 Jun 2020 08:21:54: start model_add_line... INFO @ Tue, 16 Jun 2020 08:21:54: start X-correlation... INFO @ Tue, 16 Jun 2020 08:21:54: end of X-cor INFO @ Tue, 16 Jun 2020 08:21:54: #2 finished! INFO @ Tue, 16 Jun 2020 08:21:54: #2 predicted fragment length is 57 bps INFO @ Tue, 16 Jun 2020 08:21:54: #2 alternative fragment length(s) may be 2,57 bps INFO @ Tue, 16 Jun 2020 08:21:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX257694/SRX257694.20_model.r WARNING @ Tue, 16 Jun 2020 08:21:54: #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 08:21:54: #2 You may need to consider one of the other alternative d(s): 2,57 WARNING @ Tue, 16 Jun 2020 08:21:54: #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 08:21:54: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:21:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:22:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257694/SRX257694.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:22:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257694/SRX257694.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:22:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257694/SRX257694.10_summits.bed INFO @ Tue, 16 Jun 2020 08:22:09: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1307 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:22:23: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:22:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX257694/SRX257694.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:22:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX257694/SRX257694.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:22:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX257694/SRX257694.20_summits.bed INFO @ Tue, 16 Jun 2020 08:22:38: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (361 records, 4 fields): 2 millis CompletedMACS2peakCalling