Job ID = 8070299 SRX = SRX7217784 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 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: 00:14:52 8765041 reads; of these: 8765041 (100.00%) were paired; of these: 1665173 (19.00%) aligned concordantly 0 times 6331737 (72.24%) aligned concordantly exactly 1 time 768131 (8.76%) aligned concordantly >1 times ---- 1665173 pairs aligned concordantly 0 times; of these: 535080 (32.13%) aligned discordantly 1 time ---- 1130093 pairs aligned 0 times concordantly or discordantly; of these: 2260186 mates make up the pairs; of these: 2023815 (89.54%) aligned 0 times 132518 (5.86%) aligned exactly 1 time 103853 (4.59%) aligned >1 times 88.46% overall alignment rate Time searching: 00:14:52 Overall time: 00:14:52 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 12 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 1494239 / 7592348 = 0.1968 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 @ Sat, 08 Aug 2020 13:23:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7217784/SRX7217784.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7217784/SRX7217784.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7217784/SRX7217784.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7217784/SRX7217784.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 @ Sat, 08 Aug 2020 13:23:22: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:23:22: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:23:29: 1000000 INFO @ Sat, 08 Aug 2020 13:23:37: 2000000 INFO @ Sat, 08 Aug 2020 13:23:45: 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 @ Sat, 08 Aug 2020 13:23:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7217784/SRX7217784.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7217784/SRX7217784.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7217784/SRX7217784.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7217784/SRX7217784.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 @ Sat, 08 Aug 2020 13:23:52: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:23:52: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:23:53: 4000000 INFO @ Sat, 08 Aug 2020 13:23:59: 1000000 INFO @ Sat, 08 Aug 2020 13:24:01: 5000000 INFO @ Sat, 08 Aug 2020 13:24:07: 2000000 INFO @ Sat, 08 Aug 2020 13:24:09: 6000000 INFO @ Sat, 08 Aug 2020 13:24:15: 3000000 INFO @ Sat, 08 Aug 2020 13:24:17: 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 @ Sat, 08 Aug 2020 13:24:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7217784/SRX7217784.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7217784/SRX7217784.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7217784/SRX7217784.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7217784/SRX7217784.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 @ Sat, 08 Aug 2020 13:24:22: #1 read tag files... INFO @ Sat, 08 Aug 2020 13:24:22: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 13:24:23: 4000000 INFO @ Sat, 08 Aug 2020 13:24:25: 8000000 INFO @ Sat, 08 Aug 2020 13:24:29: 1000000 INFO @ Sat, 08 Aug 2020 13:24:31: 5000000 INFO @ Sat, 08 Aug 2020 13:24:33: 9000000 INFO @ Sat, 08 Aug 2020 13:24:37: 2000000 INFO @ Sat, 08 Aug 2020 13:24:40: 6000000 INFO @ Sat, 08 Aug 2020 13:24:41: 10000000 INFO @ Sat, 08 Aug 2020 13:24:45: 3000000 INFO @ Sat, 08 Aug 2020 13:24:48: 7000000 INFO @ Sat, 08 Aug 2020 13:24:49: 11000000 INFO @ Sat, 08 Aug 2020 13:24:53: 4000000 INFO @ Sat, 08 Aug 2020 13:24:56: 8000000 INFO @ Sat, 08 Aug 2020 13:24:58: 12000000 INFO @ Sat, 08 Aug 2020 13:25:01: 5000000 INFO @ Sat, 08 Aug 2020 13:25:02: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:25:02: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:25:02: #1 total tags in treatment: 5674368 INFO @ Sat, 08 Aug 2020 13:25:02: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:25:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 13:25:02: #1 tags after filtering in treatment: 5079116 INFO @ Sat, 08 Aug 2020 13:25:02: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 08 Aug 2020 13:25:02: #1 finished! INFO @ Sat, 08 Aug 2020 13:25:02: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:25:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:25:02: #2 number of paired peaks: 1188 INFO @ Sat, 08 Aug 2020 13:25:02: start model_add_line... INFO @ Sat, 08 Aug 2020 13:25:02: start X-correlation... INFO @ Sat, 08 Aug 2020 13:25:02: end of X-cor INFO @ Sat, 08 Aug 2020 13:25:02: #2 finished! INFO @ Sat, 08 Aug 2020 13:25:02: #2 predicted fragment length is 210 bps INFO @ Sat, 08 Aug 2020 13:25:02: #2 alternative fragment length(s) may be 210 bps INFO @ Sat, 08 Aug 2020 13:25:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7217784/SRX7217784.05_model.r WARNING @ Sat, 08 Aug 2020 13:25:02: #2 Since the d (210) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:25:02: #2 You may need to consider one of the other alternative d(s): 210 WARNING @ Sat, 08 Aug 2020 13:25:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Aug 2020 13:25:02: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:25:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:25:04: 9000000 INFO @ Sat, 08 Aug 2020 13:25:10: 6000000 INFO @ Sat, 08 Aug 2020 13:25:12: 10000000 INFO @ Sat, 08 Aug 2020 13:25:15: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:25:18: 7000000 INFO @ Sat, 08 Aug 2020 13:25:20: 11000000 INFO @ Sat, 08 Aug 2020 13:25:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7217784/SRX7217784.05_peaks.xls INFO @ Sat, 08 Aug 2020 13:25:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7217784/SRX7217784.05_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:25:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7217784/SRX7217784.05_summits.bed INFO @ Sat, 08 Aug 2020 13:25:21: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4803 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 13:25:26: 8000000 INFO @ Sat, 08 Aug 2020 13:25:28: 12000000 INFO @ Sat, 08 Aug 2020 13:25:32: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:25:32: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:25:32: #1 total tags in treatment: 5674368 INFO @ Sat, 08 Aug 2020 13:25:32: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:25:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 13:25:32: #1 tags after filtering in treatment: 5079116 INFO @ Sat, 08 Aug 2020 13:25:32: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 08 Aug 2020 13:25:32: #1 finished! INFO @ Sat, 08 Aug 2020 13:25:32: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:25:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:25:33: #2 number of paired peaks: 1188 INFO @ Sat, 08 Aug 2020 13:25:33: start model_add_line... INFO @ Sat, 08 Aug 2020 13:25:33: start X-correlation... INFO @ Sat, 08 Aug 2020 13:25:33: end of X-cor INFO @ Sat, 08 Aug 2020 13:25:33: #2 finished! INFO @ Sat, 08 Aug 2020 13:25:33: #2 predicted fragment length is 210 bps INFO @ Sat, 08 Aug 2020 13:25:33: #2 alternative fragment length(s) may be 210 bps INFO @ Sat, 08 Aug 2020 13:25:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7217784/SRX7217784.10_model.r WARNING @ Sat, 08 Aug 2020 13:25:33: #2 Since the d (210) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:25:33: #2 You may need to consider one of the other alternative d(s): 210 WARNING @ Sat, 08 Aug 2020 13:25:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Aug 2020 13:25:33: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:25:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 13:25:34: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 08 Aug 2020 13:25:41: 10000000 INFO @ Sat, 08 Aug 2020 13:25:45: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:25:49: 11000000 INFO @ Sat, 08 Aug 2020 13:25:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7217784/SRX7217784.10_peaks.xls INFO @ Sat, 08 Aug 2020 13:25:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7217784/SRX7217784.10_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:25:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7217784/SRX7217784.10_summits.bed INFO @ Sat, 08 Aug 2020 13:25:51: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (2817 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 13:25:57: 12000000 INFO @ Sat, 08 Aug 2020 13:26:01: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 13:26:01: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 13:26:01: #1 total tags in treatment: 5674368 INFO @ Sat, 08 Aug 2020 13:26:01: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 13:26:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 13:26:01: #1 tags after filtering in treatment: 5079116 INFO @ Sat, 08 Aug 2020 13:26:01: #1 Redundant rate of treatment: 0.10 INFO @ Sat, 08 Aug 2020 13:26:01: #1 finished! INFO @ Sat, 08 Aug 2020 13:26:01: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 13:26:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 13:26:01: #2 number of paired peaks: 1188 INFO @ Sat, 08 Aug 2020 13:26:01: start model_add_line... INFO @ Sat, 08 Aug 2020 13:26:01: start X-correlation... INFO @ Sat, 08 Aug 2020 13:26:01: end of X-cor INFO @ Sat, 08 Aug 2020 13:26:01: #2 finished! INFO @ Sat, 08 Aug 2020 13:26:01: #2 predicted fragment length is 210 bps INFO @ Sat, 08 Aug 2020 13:26:01: #2 alternative fragment length(s) may be 210 bps INFO @ Sat, 08 Aug 2020 13:26:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7217784/SRX7217784.20_model.r WARNING @ Sat, 08 Aug 2020 13:26:01: #2 Since the d (210) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 13:26:01: #2 You may need to consider one of the other alternative d(s): 210 WARNING @ Sat, 08 Aug 2020 13:26:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Aug 2020 13:26:01: #3 Call peaks... INFO @ Sat, 08 Aug 2020 13:26:01: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 08 Aug 2020 13:26:13: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 13:26:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7217784/SRX7217784.20_peaks.xls INFO @ Sat, 08 Aug 2020 13:26:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7217784/SRX7217784.20_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 13:26:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7217784/SRX7217784.20_summits.bed INFO @ Sat, 08 Aug 2020 13:26:19: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1247 records, 4 fields): 3 millis CompletedMACS2peakCalling