Job ID = 12265320 SRX = SRX7246267 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:16:22 11752793 reads; of these: 11752793 (100.00%) were paired; of these: 641747 (5.46%) aligned concordantly 0 times 9984972 (84.96%) aligned concordantly exactly 1 time 1126074 (9.58%) aligned concordantly >1 times ---- 641747 pairs aligned concordantly 0 times; of these: 233799 (36.43%) aligned discordantly 1 time ---- 407948 pairs aligned 0 times concordantly or discordantly; of these: 815896 mates make up the pairs; of these: 575576 (70.55%) aligned 0 times 163669 (20.06%) aligned exactly 1 time 76651 (9.39%) aligned >1 times 97.55% overall alignment rate Time searching: 00:16:23 Overall time: 00:16:23 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] 2696612 / 7964156 = 0.3386 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:06:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7246267/SRX7246267.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7246267/SRX7246267.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7246267/SRX7246267.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7246267/SRX7246267.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, 03 Apr 2021 07:06:54: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:06:54: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:07:04: 1000000 INFO @ Sat, 03 Apr 2021 07:07:13: 2000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:07:21: 3000000 INFO @ Sat, 03 Apr 2021 07:07:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7246267/SRX7246267.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7246267/SRX7246267.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7246267/SRX7246267.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7246267/SRX7246267.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, 03 Apr 2021 07:07:23: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:07:23: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:07:31: 4000000 INFO @ Sat, 03 Apr 2021 07:07:32: 1000000 INFO @ Sat, 03 Apr 2021 07:07:41: 5000000 INFO @ Sat, 03 Apr 2021 07:07:41: 2000000 INFO @ Sat, 03 Apr 2021 07:07:50: 6000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:07:50: 3000000 INFO @ Sat, 03 Apr 2021 07:07:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7246267/SRX7246267.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7246267/SRX7246267.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7246267/SRX7246267.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7246267/SRX7246267.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, 03 Apr 2021 07:07:53: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:07:53: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:07:58: 7000000 INFO @ Sat, 03 Apr 2021 07:08:00: 4000000 INFO @ Sat, 03 Apr 2021 07:08:03: 1000000 INFO @ Sat, 03 Apr 2021 07:08:07: 8000000 INFO @ Sat, 03 Apr 2021 07:08:10: 5000000 INFO @ Sat, 03 Apr 2021 07:08:12: 2000000 INFO @ Sat, 03 Apr 2021 07:08:16: 9000000 INFO @ Sat, 03 Apr 2021 07:08:18: 6000000 INFO @ Sat, 03 Apr 2021 07:08:20: 3000000 INFO @ Sat, 03 Apr 2021 07:08:25: 10000000 INFO @ Sat, 03 Apr 2021 07:08:27: 7000000 INFO @ Sat, 03 Apr 2021 07:08:30: 4000000 INFO @ Sat, 03 Apr 2021 07:08:34: 11000000 INFO @ Sat, 03 Apr 2021 07:08:36: 8000000 INFO @ Sat, 03 Apr 2021 07:08:39: 5000000 INFO @ Sat, 03 Apr 2021 07:08:44: 12000000 INFO @ Sat, 03 Apr 2021 07:08:44: 9000000 INFO @ Sat, 03 Apr 2021 07:08:48: 6000000 INFO @ Sat, 03 Apr 2021 07:08:53: 10000000 INFO @ Sat, 03 Apr 2021 07:08:53: 13000000 INFO @ Sat, 03 Apr 2021 07:08:57: 7000000 INFO @ Sat, 03 Apr 2021 07:09:02: 11000000 INFO @ Sat, 03 Apr 2021 07:09:02: 14000000 INFO @ Sat, 03 Apr 2021 07:09:06: 8000000 INFO @ Sat, 03 Apr 2021 07:09:11: 12000000 INFO @ Sat, 03 Apr 2021 07:09:12: 15000000 INFO @ Sat, 03 Apr 2021 07:09:14: 9000000 INFO @ Sat, 03 Apr 2021 07:09:18: 13000000 INFO @ Sat, 03 Apr 2021 07:09:20: 16000000 INFO @ Sat, 03 Apr 2021 07:09:23: 10000000 INFO @ Sat, 03 Apr 2021 07:09:26: 14000000 INFO @ Sat, 03 Apr 2021 07:09:28: 17000000 INFO @ Sat, 03 Apr 2021 07:09:32: 11000000 INFO @ Sat, 03 Apr 2021 07:09:33: #1 tag size is determined as 95 bps INFO @ Sat, 03 Apr 2021 07:09:33: #1 tag size = 95 INFO @ Sat, 03 Apr 2021 07:09:33: #1 total tags in treatment: 8419119 INFO @ Sat, 03 Apr 2021 07:09:33: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:09:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:09:33: #1 tags after filtering in treatment: 4381018 INFO @ Sat, 03 Apr 2021 07:09:33: #1 Redundant rate of treatment: 0.48 INFO @ Sat, 03 Apr 2021 07:09:33: #1 finished! INFO @ Sat, 03 Apr 2021 07:09:33: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:09:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:09:34: #2 number of paired peaks: 3780 INFO @ Sat, 03 Apr 2021 07:09:34: start model_add_line... INFO @ Sat, 03 Apr 2021 07:09:34: start X-correlation... INFO @ Sat, 03 Apr 2021 07:09:34: end of X-cor INFO @ Sat, 03 Apr 2021 07:09:34: #2 finished! INFO @ Sat, 03 Apr 2021 07:09:34: #2 predicted fragment length is 106 bps INFO @ Sat, 03 Apr 2021 07:09:34: #2 alternative fragment length(s) may be 106 bps INFO @ Sat, 03 Apr 2021 07:09:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7246267/SRX7246267.05_model.r WARNING @ Sat, 03 Apr 2021 07:09:34: #2 Since the d (106) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:09:34: #2 You may need to consider one of the other alternative d(s): 106 WARNING @ Sat, 03 Apr 2021 07:09:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:09:34: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:09:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:09:34: 15000000 INFO @ Sat, 03 Apr 2021 07:09:40: 12000000 INFO @ Sat, 03 Apr 2021 07:09:42: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 07:09:49: 13000000 INFO @ Sat, 03 Apr 2021 07:09:49: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:09:49: 17000000 INFO @ Sat, 03 Apr 2021 07:09:53: #1 tag size is determined as 95 bps INFO @ Sat, 03 Apr 2021 07:09:53: #1 tag size = 95 INFO @ Sat, 03 Apr 2021 07:09:53: #1 total tags in treatment: 8419119 INFO @ Sat, 03 Apr 2021 07:09:53: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:09:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:09:53: #1 tags after filtering in treatment: 4381018 INFO @ Sat, 03 Apr 2021 07:09:53: #1 Redundant rate of treatment: 0.48 INFO @ Sat, 03 Apr 2021 07:09:53: #1 finished! INFO @ Sat, 03 Apr 2021 07:09:53: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:09:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:09:54: #2 number of paired peaks: 3780 INFO @ Sat, 03 Apr 2021 07:09:54: start model_add_line... INFO @ Sat, 03 Apr 2021 07:09:54: start X-correlation... INFO @ Sat, 03 Apr 2021 07:09:54: end of X-cor INFO @ Sat, 03 Apr 2021 07:09:54: #2 finished! INFO @ Sat, 03 Apr 2021 07:09:54: #2 predicted fragment length is 106 bps INFO @ Sat, 03 Apr 2021 07:09:54: #2 alternative fragment length(s) may be 106 bps INFO @ Sat, 03 Apr 2021 07:09:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7246267/SRX7246267.10_model.r WARNING @ Sat, 03 Apr 2021 07:09:54: #2 Since the d (106) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:09:54: #2 You may need to consider one of the other alternative d(s): 106 WARNING @ Sat, 03 Apr 2021 07:09:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:09:54: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:09:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:09:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7246267/SRX7246267.05_peaks.xls INFO @ Sat, 03 Apr 2021 07:09:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7246267/SRX7246267.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:09:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7246267/SRX7246267.05_summits.bed INFO @ Sat, 03 Apr 2021 07:09:57: Done! pass1 - making usageList (7 chroms): 4 millis pass2 - checking and writing primary data (8535 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:09:57: 14000000 INFO @ Sat, 03 Apr 2021 07:10:06: 15000000 BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 07:10:09: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:10:14: 16000000 INFO @ Sat, 03 Apr 2021 07:10:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7246267/SRX7246267.10_peaks.xls INFO @ Sat, 03 Apr 2021 07:10:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7246267/SRX7246267.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:10:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7246267/SRX7246267.10_summits.bed INFO @ Sat, 03 Apr 2021 07:10:16: Done! pass1 - making usageList (7 chroms): 5 millis pass2 - checking and writing primary data (6208 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:10:22: 17000000 INFO @ Sat, 03 Apr 2021 07:10:27: #1 tag size is determined as 95 bps INFO @ Sat, 03 Apr 2021 07:10:27: #1 tag size = 95 INFO @ Sat, 03 Apr 2021 07:10:27: #1 total tags in treatment: 8419119 INFO @ Sat, 03 Apr 2021 07:10:27: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:10:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:10:28: #1 tags after filtering in treatment: 4381018 INFO @ Sat, 03 Apr 2021 07:10:28: #1 Redundant rate of treatment: 0.48 INFO @ Sat, 03 Apr 2021 07:10:28: #1 finished! INFO @ Sat, 03 Apr 2021 07:10:28: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:10:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:10:28: #2 number of paired peaks: 3780 INFO @ Sat, 03 Apr 2021 07:10:28: start model_add_line... INFO @ Sat, 03 Apr 2021 07:10:28: start X-correlation... INFO @ Sat, 03 Apr 2021 07:10:29: end of X-cor INFO @ Sat, 03 Apr 2021 07:10:29: #2 finished! INFO @ Sat, 03 Apr 2021 07:10:29: #2 predicted fragment length is 106 bps INFO @ Sat, 03 Apr 2021 07:10:29: #2 alternative fragment length(s) may be 106 bps INFO @ Sat, 03 Apr 2021 07:10:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7246267/SRX7246267.20_model.r WARNING @ Sat, 03 Apr 2021 07:10:29: #2 Since the d (106) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:10:29: #2 You may need to consider one of the other alternative d(s): 106 WARNING @ Sat, 03 Apr 2021 07:10:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:10:29: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:10:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:10:44: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:10:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7246267/SRX7246267.20_peaks.xls INFO @ Sat, 03 Apr 2021 07:10:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7246267/SRX7246267.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:10:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7246267/SRX7246267.20_summits.bed INFO @ Sat, 03 Apr 2021 07:10:52: Done! pass1 - making usageList (6 chroms): 3 millis pass2 - checking and writing primary data (3835 records, 4 fields): 17 millis CompletedMACS2peakCalling