Job ID = 6367171 SRX = SRX2965745 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:16:16 prefetch.2.10.7: 1) Downloading 'SRR5766330'... 2020-06-15T23:16:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:20:10 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:20:10 prefetch.2.10.7: 1) 'SRR5766330' was downloaded successfully Read 27801818 spots for SRR5766330/SRR5766330.sra Written 27801818 spots for SRR5766330/SRR5766330.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: 00:13:26 27801818 reads; of these: 27801818 (100.00%) were unpaired; of these: 961962 (3.46%) aligned 0 times 22479825 (80.86%) aligned exactly 1 time 4360031 (15.68%) aligned >1 times 96.54% overall alignment rate Time searching: 00:13:26 Overall time: 00:13:26 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] 3123109 / 26839856 = 0.1164 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 08:44:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2965745/SRX2965745.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2965745/SRX2965745.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2965745/SRX2965745.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2965745/SRX2965745.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 08:44:15: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:44:15: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:44:23: 1000000 INFO @ Tue, 16 Jun 2020 08:44:30: 2000000 INFO @ Tue, 16 Jun 2020 08:44:37: 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 08:44:44: 4000000 INFO @ Tue, 16 Jun 2020 08:44:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2965745/SRX2965745.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2965745/SRX2965745.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2965745/SRX2965745.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2965745/SRX2965745.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 08:44:45: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:44:45: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:44:52: 5000000 INFO @ Tue, 16 Jun 2020 08:44:53: 1000000 INFO @ Tue, 16 Jun 2020 08:45:00: 6000000 INFO @ Tue, 16 Jun 2020 08:45:01: 2000000 INFO @ Tue, 16 Jun 2020 08:45:09: 7000000 INFO @ Tue, 16 Jun 2020 08:45:09: 3000000 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 08:45:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2965745/SRX2965745.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2965745/SRX2965745.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2965745/SRX2965745.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2965745/SRX2965745.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 08:45:15: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:45:15: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:45:17: 8000000 INFO @ Tue, 16 Jun 2020 08:45:18: 4000000 INFO @ Tue, 16 Jun 2020 08:45:24: 1000000 INFO @ Tue, 16 Jun 2020 08:45:25: 9000000 INFO @ Tue, 16 Jun 2020 08:45:26: 5000000 INFO @ Tue, 16 Jun 2020 08:45:32: 2000000 INFO @ Tue, 16 Jun 2020 08:45:34: 10000000 INFO @ Tue, 16 Jun 2020 08:45:35: 6000000 INFO @ Tue, 16 Jun 2020 08:45:41: 3000000 INFO @ Tue, 16 Jun 2020 08:45:42: 11000000 INFO @ Tue, 16 Jun 2020 08:45:43: 7000000 INFO @ Tue, 16 Jun 2020 08:45:50: 4000000 INFO @ Tue, 16 Jun 2020 08:45:51: 12000000 INFO @ Tue, 16 Jun 2020 08:45:52: 8000000 INFO @ Tue, 16 Jun 2020 08:45:59: 5000000 INFO @ Tue, 16 Jun 2020 08:46:00: 13000000 INFO @ Tue, 16 Jun 2020 08:46:01: 9000000 INFO @ Tue, 16 Jun 2020 08:46:08: 6000000 INFO @ Tue, 16 Jun 2020 08:46:09: 14000000 INFO @ Tue, 16 Jun 2020 08:46:10: 10000000 INFO @ Tue, 16 Jun 2020 08:46:17: 7000000 INFO @ Tue, 16 Jun 2020 08:46:17: 15000000 INFO @ Tue, 16 Jun 2020 08:46:19: 11000000 INFO @ Tue, 16 Jun 2020 08:46:25: 8000000 INFO @ Tue, 16 Jun 2020 08:46:26: 16000000 INFO @ Tue, 16 Jun 2020 08:46:28: 12000000 INFO @ Tue, 16 Jun 2020 08:46:34: 9000000 INFO @ Tue, 16 Jun 2020 08:46:34: 17000000 INFO @ Tue, 16 Jun 2020 08:46:37: 13000000 INFO @ Tue, 16 Jun 2020 08:46:43: 10000000 INFO @ Tue, 16 Jun 2020 08:46:43: 18000000 INFO @ Tue, 16 Jun 2020 08:46:45: 14000000 INFO @ Tue, 16 Jun 2020 08:46:51: 11000000 INFO @ Tue, 16 Jun 2020 08:46:52: 19000000 INFO @ Tue, 16 Jun 2020 08:46:54: 15000000 INFO @ Tue, 16 Jun 2020 08:47:00: 12000000 INFO @ Tue, 16 Jun 2020 08:47:00: 20000000 INFO @ Tue, 16 Jun 2020 08:47:03: 16000000 INFO @ Tue, 16 Jun 2020 08:47:09: 21000000 INFO @ Tue, 16 Jun 2020 08:47:09: 13000000 INFO @ Tue, 16 Jun 2020 08:47:12: 17000000 INFO @ Tue, 16 Jun 2020 08:47:18: 22000000 INFO @ Tue, 16 Jun 2020 08:47:18: 14000000 INFO @ Tue, 16 Jun 2020 08:47:21: 18000000 INFO @ Tue, 16 Jun 2020 08:47:27: 23000000 INFO @ Tue, 16 Jun 2020 08:47:27: 15000000 INFO @ Tue, 16 Jun 2020 08:47:30: 19000000 INFO @ Tue, 16 Jun 2020 08:47:33: #1 tag size is determined as 101 bps INFO @ Tue, 16 Jun 2020 08:47:33: #1 tag size = 101 INFO @ Tue, 16 Jun 2020 08:47:33: #1 total tags in treatment: 23716747 INFO @ Tue, 16 Jun 2020 08:47:33: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:47:33: #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 08:47:34: #1 tags after filtering in treatment: 23716747 INFO @ Tue, 16 Jun 2020 08:47:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:47:34: #1 finished! INFO @ Tue, 16 Jun 2020 08:47:34: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:47:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:47:35: #2 number of paired peaks: 116 WARNING @ Tue, 16 Jun 2020 08:47:35: Fewer paired peaks (116) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 116 pairs to build model! INFO @ Tue, 16 Jun 2020 08:47:35: start model_add_line... INFO @ Tue, 16 Jun 2020 08:47:35: start X-correlation... INFO @ Tue, 16 Jun 2020 08:47:35: end of X-cor INFO @ Tue, 16 Jun 2020 08:47:35: #2 finished! INFO @ Tue, 16 Jun 2020 08:47:35: #2 predicted fragment length is 87 bps INFO @ Tue, 16 Jun 2020 08:47:35: #2 alternative fragment length(s) may be 2,87 bps INFO @ Tue, 16 Jun 2020 08:47:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2965745/SRX2965745.05_model.r WARNING @ Tue, 16 Jun 2020 08:47:35: #2 Since the d (87) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:47:35: #2 You may need to consider one of the other alternative d(s): 2,87 WARNING @ Tue, 16 Jun 2020 08:47:35: #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 08:47:35: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:47:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:47:36: 16000000 INFO @ Tue, 16 Jun 2020 08:47:39: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:47:44: 17000000 INFO @ Tue, 16 Jun 2020 08:47:47: 21000000 INFO @ Tue, 16 Jun 2020 08:47:53: 18000000 INFO @ Tue, 16 Jun 2020 08:47:55: 22000000 INFO @ Tue, 16 Jun 2020 08:48:01: 19000000 INFO @ Tue, 16 Jun 2020 08:48:04: 23000000 INFO @ Tue, 16 Jun 2020 08:48:09: 20000000 INFO @ Tue, 16 Jun 2020 08:48:10: #1 tag size is determined as 101 bps INFO @ Tue, 16 Jun 2020 08:48:10: #1 tag size = 101 INFO @ Tue, 16 Jun 2020 08:48:10: #1 total tags in treatment: 23716747 INFO @ Tue, 16 Jun 2020 08:48:10: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:48:10: #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 08:48:10: #1 tags after filtering in treatment: 23716747 INFO @ Tue, 16 Jun 2020 08:48:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:48:10: #1 finished! INFO @ Tue, 16 Jun 2020 08:48:10: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:48:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:48:11: #2 number of paired peaks: 116 WARNING @ Tue, 16 Jun 2020 08:48:11: Fewer paired peaks (116) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 116 pairs to build model! INFO @ Tue, 16 Jun 2020 08:48:11: start model_add_line... INFO @ Tue, 16 Jun 2020 08:48:12: start X-correlation... INFO @ Tue, 16 Jun 2020 08:48:12: end of X-cor INFO @ Tue, 16 Jun 2020 08:48:12: #2 finished! INFO @ Tue, 16 Jun 2020 08:48:12: #2 predicted fragment length is 87 bps INFO @ Tue, 16 Jun 2020 08:48:12: #2 alternative fragment length(s) may be 2,87 bps INFO @ Tue, 16 Jun 2020 08:48:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2965745/SRX2965745.10_model.r WARNING @ Tue, 16 Jun 2020 08:48:12: #2 Since the d (87) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:48:12: #2 You may need to consider one of the other alternative d(s): 2,87 WARNING @ Tue, 16 Jun 2020 08:48:12: #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 08:48:12: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:48:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:48:14: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:48:17: 21000000 INFO @ Tue, 16 Jun 2020 08:48:25: 22000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:48:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2965745/SRX2965745.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:48:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2965745/SRX2965745.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:48:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2965745/SRX2965745.05_summits.bed INFO @ Tue, 16 Jun 2020 08:48:32: Done! INFO @ Tue, 16 Jun 2020 08:48:32: 23000000 pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (592 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:48:38: #1 tag size is determined as 101 bps INFO @ Tue, 16 Jun 2020 08:48:38: #1 tag size = 101 INFO @ Tue, 16 Jun 2020 08:48:38: #1 total tags in treatment: 23716747 INFO @ Tue, 16 Jun 2020 08:48:38: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:48:38: #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 08:48:38: #1 tags after filtering in treatment: 23716747 INFO @ Tue, 16 Jun 2020 08:48:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:48:38: #1 finished! INFO @ Tue, 16 Jun 2020 08:48:38: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:48:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:48:40: #2 number of paired peaks: 116 WARNING @ Tue, 16 Jun 2020 08:48:40: Fewer paired peaks (116) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 116 pairs to build model! INFO @ Tue, 16 Jun 2020 08:48:40: start model_add_line... INFO @ Tue, 16 Jun 2020 08:48:40: start X-correlation... INFO @ Tue, 16 Jun 2020 08:48:40: end of X-cor INFO @ Tue, 16 Jun 2020 08:48:40: #2 finished! INFO @ Tue, 16 Jun 2020 08:48:40: #2 predicted fragment length is 87 bps INFO @ Tue, 16 Jun 2020 08:48:40: #2 alternative fragment length(s) may be 2,87 bps INFO @ Tue, 16 Jun 2020 08:48:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2965745/SRX2965745.20_model.r WARNING @ Tue, 16 Jun 2020 08:48:40: #2 Since the d (87) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:48:40: #2 You may need to consider one of the other alternative d(s): 2,87 WARNING @ Tue, 16 Jun 2020 08:48:40: #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 08:48:40: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:48:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:48:51: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:49:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2965745/SRX2965745.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:49:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2965745/SRX2965745.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:49:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2965745/SRX2965745.10_summits.bed INFO @ Tue, 16 Jun 2020 08:49:09: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (432 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:49:18: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:49:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2965745/SRX2965745.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:49:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2965745/SRX2965745.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:49:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2965745/SRX2965745.20_summits.bed INFO @ Tue, 16 Jun 2020 08:49:37: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (221 records, 4 fields): 2 millis CompletedMACS2peakCalling