Job ID = 6368806 SRX = SRX5729148 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:34:10 prefetch.2.10.7: 1) Downloading 'SRR8949160'... 2020-06-16T00:34:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:35:18 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:35:19 prefetch.2.10.7: 'SRR8949160' is valid 2020-06-16T00:35:19 prefetch.2.10.7: 1) 'SRR8949160' was downloaded successfully 2020-06-16T00:35:19 prefetch.2.10.7: 'SRR8949160' has 0 unresolved dependencies Read 11313276 spots for SRR8949160/SRR8949160.sra Written 11313276 spots for SRR8949160/SRR8949160.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: 00:03:52 11313276 reads; of these: 11313276 (100.00%) were unpaired; of these: 1216987 (10.76%) aligned 0 times 8238167 (72.82%) aligned exactly 1 time 1858122 (16.42%) aligned >1 times 89.24% overall alignment rate Time searching: 00:03:52 Overall time: 00:03:52 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] 867479 / 10096289 = 0.0859 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 09:42:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5729148/SRX5729148.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5729148/SRX5729148.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5729148/SRX5729148.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5729148/SRX5729148.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 09:42:47: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:42:47: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:42:55: 1000000 INFO @ Tue, 16 Jun 2020 09:43:03: 2000000 INFO @ Tue, 16 Jun 2020 09:43:11: 3000000 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 09:43:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5729148/SRX5729148.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5729148/SRX5729148.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5729148/SRX5729148.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5729148/SRX5729148.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 09:43:17: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:43:17: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:43:19: 4000000 INFO @ Tue, 16 Jun 2020 09:43:25: 1000000 INFO @ Tue, 16 Jun 2020 09:43:27: 5000000 INFO @ Tue, 16 Jun 2020 09:43:34: 2000000 INFO @ Tue, 16 Jun 2020 09:43:35: 6000000 INFO @ Tue, 16 Jun 2020 09:43:42: 3000000 INFO @ Tue, 16 Jun 2020 09:43:43: 7000000 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 09:43:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5729148/SRX5729148.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5729148/SRX5729148.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5729148/SRX5729148.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5729148/SRX5729148.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 09:43:47: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:43:47: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:43:50: 4000000 INFO @ Tue, 16 Jun 2020 09:43:51: 8000000 INFO @ Tue, 16 Jun 2020 09:43:55: 1000000 INFO @ Tue, 16 Jun 2020 09:43:58: 5000000 INFO @ Tue, 16 Jun 2020 09:43:59: 9000000 INFO @ Tue, 16 Jun 2020 09:44:01: #1 tag size is determined as 75 bps INFO @ Tue, 16 Jun 2020 09:44:01: #1 tag size = 75 INFO @ Tue, 16 Jun 2020 09:44:01: #1 total tags in treatment: 9228810 INFO @ Tue, 16 Jun 2020 09:44:01: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:44:01: #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 09:44:01: #1 tags after filtering in treatment: 9228810 INFO @ Tue, 16 Jun 2020 09:44:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:44:01: #1 finished! INFO @ Tue, 16 Jun 2020 09:44:01: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:44:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:44:01: #2 number of paired peaks: 338 WARNING @ Tue, 16 Jun 2020 09:44:01: Fewer paired peaks (338) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 338 pairs to build model! INFO @ Tue, 16 Jun 2020 09:44:01: start model_add_line... INFO @ Tue, 16 Jun 2020 09:44:02: start X-correlation... INFO @ Tue, 16 Jun 2020 09:44:02: end of X-cor INFO @ Tue, 16 Jun 2020 09:44:02: #2 finished! INFO @ Tue, 16 Jun 2020 09:44:02: #2 predicted fragment length is 70 bps INFO @ Tue, 16 Jun 2020 09:44:02: #2 alternative fragment length(s) may be 4,70,528 bps INFO @ Tue, 16 Jun 2020 09:44:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5729148/SRX5729148.05_model.r WARNING @ Tue, 16 Jun 2020 09:44:02: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:44:02: #2 You may need to consider one of the other alternative d(s): 4,70,528 WARNING @ Tue, 16 Jun 2020 09:44:02: #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 09:44:02: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:44:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:44:03: 2000000 INFO @ Tue, 16 Jun 2020 09:44:06: 6000000 INFO @ Tue, 16 Jun 2020 09:44:10: 3000000 INFO @ Tue, 16 Jun 2020 09:44:13: 7000000 INFO @ Tue, 16 Jun 2020 09:44:17: 4000000 INFO @ Tue, 16 Jun 2020 09:44:21: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:44:21: 8000000 INFO @ Tue, 16 Jun 2020 09:44:25: 5000000 INFO @ Tue, 16 Jun 2020 09:44:29: 9000000 INFO @ Tue, 16 Jun 2020 09:44:31: #1 tag size is determined as 75 bps INFO @ Tue, 16 Jun 2020 09:44:31: #1 tag size = 75 INFO @ Tue, 16 Jun 2020 09:44:31: #1 total tags in treatment: 9228810 INFO @ Tue, 16 Jun 2020 09:44:31: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:44:31: #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 09:44:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5729148/SRX5729148.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:44:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5729148/SRX5729148.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:44:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5729148/SRX5729148.05_summits.bed INFO @ Tue, 16 Jun 2020 09:44:31: Done! INFO @ Tue, 16 Jun 2020 09:44:31: #1 tags after filtering in treatment: 9228810 INFO @ Tue, 16 Jun 2020 09:44:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:44:31: #1 finished! INFO @ Tue, 16 Jun 2020 09:44:31: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:44:31: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (923 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:44:32: #2 number of paired peaks: 338 WARNING @ Tue, 16 Jun 2020 09:44:32: Fewer paired peaks (338) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 338 pairs to build model! INFO @ Tue, 16 Jun 2020 09:44:32: start model_add_line... INFO @ Tue, 16 Jun 2020 09:44:32: start X-correlation... INFO @ Tue, 16 Jun 2020 09:44:32: end of X-cor INFO @ Tue, 16 Jun 2020 09:44:32: #2 finished! INFO @ Tue, 16 Jun 2020 09:44:32: #2 predicted fragment length is 70 bps INFO @ Tue, 16 Jun 2020 09:44:32: #2 alternative fragment length(s) may be 4,70,528 bps INFO @ Tue, 16 Jun 2020 09:44:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5729148/SRX5729148.10_model.r WARNING @ Tue, 16 Jun 2020 09:44:32: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:44:32: #2 You may need to consider one of the other alternative d(s): 4,70,528 WARNING @ Tue, 16 Jun 2020 09:44:32: #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 09:44:32: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:44:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:44:32: 6000000 INFO @ Tue, 16 Jun 2020 09:44:39: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:44:45: 8000000 INFO @ Tue, 16 Jun 2020 09:44:51: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:44:52: 9000000 INFO @ Tue, 16 Jun 2020 09:44:53: #1 tag size is determined as 75 bps INFO @ Tue, 16 Jun 2020 09:44:53: #1 tag size = 75 INFO @ Tue, 16 Jun 2020 09:44:53: #1 total tags in treatment: 9228810 INFO @ Tue, 16 Jun 2020 09:44:53: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:44:53: #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 09:44:53: #1 tags after filtering in treatment: 9228810 INFO @ Tue, 16 Jun 2020 09:44:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:44:53: #1 finished! INFO @ Tue, 16 Jun 2020 09:44:53: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:44:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:44:54: #2 number of paired peaks: 338 WARNING @ Tue, 16 Jun 2020 09:44:54: Fewer paired peaks (338) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 338 pairs to build model! INFO @ Tue, 16 Jun 2020 09:44:54: start model_add_line... INFO @ Tue, 16 Jun 2020 09:44:54: start X-correlation... INFO @ Tue, 16 Jun 2020 09:44:54: end of X-cor INFO @ Tue, 16 Jun 2020 09:44:54: #2 finished! INFO @ Tue, 16 Jun 2020 09:44:54: #2 predicted fragment length is 70 bps INFO @ Tue, 16 Jun 2020 09:44:54: #2 alternative fragment length(s) may be 4,70,528 bps INFO @ Tue, 16 Jun 2020 09:44:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5729148/SRX5729148.20_model.r WARNING @ Tue, 16 Jun 2020 09:44:54: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:44:54: #2 You may need to consider one of the other alternative d(s): 4,70,528 WARNING @ Tue, 16 Jun 2020 09:44:54: #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 09:44:54: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:44:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:45:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5729148/SRX5729148.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:45:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5729148/SRX5729148.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:45:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5729148/SRX5729148.10_summits.bed INFO @ Tue, 16 Jun 2020 09:45:00: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (466 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:45:12: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:45:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5729148/SRX5729148.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:45:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5729148/SRX5729148.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:45:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5729148/SRX5729148.20_summits.bed INFO @ Tue, 16 Jun 2020 09:45:22: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (213 records, 4 fields): 1 millis CompletedMACS2peakCalling