Job ID = 14159663 SRX = SRX8845621 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: 00:00:01 Multiseed full-index search: 00:10:03 8944770 reads; of these: 8944770 (100.00%) were paired; of these: 3132673 (35.02%) aligned concordantly 0 times 5112450 (57.16%) aligned concordantly exactly 1 time 699647 (7.82%) aligned concordantly >1 times ---- 3132673 pairs aligned concordantly 0 times; of these: 1038382 (33.15%) aligned discordantly 1 time ---- 2094291 pairs aligned 0 times concordantly or discordantly; of these: 4188582 mates make up the pairs; of these: 3657101 (87.31%) aligned 0 times 282677 (6.75%) aligned exactly 1 time 248804 (5.94%) aligned >1 times 79.56% overall alignment rate Time searching: 00:10:04 Overall time: 00:10:04 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_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] 1381234 / 6782357 = 0.2037 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 00:23:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8845621/SRX8845621.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8845621/SRX8845621.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8845621/SRX8845621.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8845621/SRX8845621.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 @ Thu, 09 Dec 2021 00:23:20: #1 read tag files... INFO @ Thu, 09 Dec 2021 00:23:20: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 00:23:28: 1000000 INFO @ Thu, 09 Dec 2021 00:23:35: 2000000 INFO @ Thu, 09 Dec 2021 00:23:43: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 00:23:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8845621/SRX8845621.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8845621/SRX8845621.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8845621/SRX8845621.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8845621/SRX8845621.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 @ Thu, 09 Dec 2021 00:23:49: #1 read tag files... INFO @ Thu, 09 Dec 2021 00:23:49: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 00:23:50: 4000000 INFO @ Thu, 09 Dec 2021 00:23:58: 1000000 INFO @ Thu, 09 Dec 2021 00:23:58: 5000000 INFO @ Thu, 09 Dec 2021 00:24:06: 6000000 INFO @ Thu, 09 Dec 2021 00:24:07: 2000000 INFO @ Thu, 09 Dec 2021 00:24:14: 7000000 INFO @ Thu, 09 Dec 2021 00:24:16: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Thu, 09 Dec 2021 00:24:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8845621/SRX8845621.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8845621/SRX8845621.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8845621/SRX8845621.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8845621/SRX8845621.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 @ Thu, 09 Dec 2021 00:24:19: #1 read tag files... INFO @ Thu, 09 Dec 2021 00:24:19: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 00:24:22: 8000000 INFO @ Thu, 09 Dec 2021 00:24:25: 4000000 INFO @ Thu, 09 Dec 2021 00:24:28: 1000000 INFO @ Thu, 09 Dec 2021 00:24:30: 9000000 INFO @ Thu, 09 Dec 2021 00:24:34: 5000000 INFO @ Thu, 09 Dec 2021 00:24:37: 2000000 INFO @ Thu, 09 Dec 2021 00:24:37: 10000000 INFO @ Thu, 09 Dec 2021 00:24:43: 6000000 INFO @ Thu, 09 Dec 2021 00:24:45: 11000000 INFO @ Thu, 09 Dec 2021 00:24:46: 3000000 INFO @ Thu, 09 Dec 2021 00:24:49: #1 tag size is determined as 75 bps INFO @ Thu, 09 Dec 2021 00:24:49: #1 tag size = 75 INFO @ Thu, 09 Dec 2021 00:24:49: #1 total tags in treatment: 4625094 INFO @ Thu, 09 Dec 2021 00:24:49: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 00:24:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 00:24:49: #1 tags after filtering in treatment: 3364978 INFO @ Thu, 09 Dec 2021 00:24:49: #1 Redundant rate of treatment: 0.27 INFO @ Thu, 09 Dec 2021 00:24:49: #1 finished! INFO @ Thu, 09 Dec 2021 00:24:49: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 00:24:49: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 00:24:50: #2 number of paired peaks: 3050 INFO @ Thu, 09 Dec 2021 00:24:50: start model_add_line... INFO @ Thu, 09 Dec 2021 00:24:50: start X-correlation... INFO @ Thu, 09 Dec 2021 00:24:50: end of X-cor INFO @ Thu, 09 Dec 2021 00:24:50: #2 finished! INFO @ Thu, 09 Dec 2021 00:24:50: #2 predicted fragment length is 119 bps INFO @ Thu, 09 Dec 2021 00:24:50: #2 alternative fragment length(s) may be 119 bps INFO @ Thu, 09 Dec 2021 00:24:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8845621/SRX8845621.05_model.r WARNING @ Thu, 09 Dec 2021 00:24:50: #2 Since the d (119) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 00:24:50: #2 You may need to consider one of the other alternative d(s): 119 WARNING @ Thu, 09 Dec 2021 00:24:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 00:24:50: #3 Call peaks... INFO @ Thu, 09 Dec 2021 00:24:50: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 00:24:52: 7000000 INFO @ Thu, 09 Dec 2021 00:24:55: 4000000 INFO @ Thu, 09 Dec 2021 00:25:01: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 00:25:01: 8000000 INFO @ Thu, 09 Dec 2021 00:25:05: 5000000 INFO @ Thu, 09 Dec 2021 00:25:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8845621/SRX8845621.05_peaks.xls INFO @ Thu, 09 Dec 2021 00:25:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8845621/SRX8845621.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 00:25:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8845621/SRX8845621.05_summits.bed INFO @ Thu, 09 Dec 2021 00:25:07: Done! pass1 - making usageList (7 chroms): 4 millis pass2 - checking and writing primary data (7419 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 00:25:10: 9000000 INFO @ Thu, 09 Dec 2021 00:25:15: 6000000 INFO @ Thu, 09 Dec 2021 00:25:19: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 00:25:24: 7000000 INFO @ Thu, 09 Dec 2021 00:25:28: 11000000 INFO @ Thu, 09 Dec 2021 00:25:32: #1 tag size is determined as 75 bps INFO @ Thu, 09 Dec 2021 00:25:32: #1 tag size = 75 INFO @ Thu, 09 Dec 2021 00:25:32: #1 total tags in treatment: 4625094 INFO @ Thu, 09 Dec 2021 00:25:32: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 00:25:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 00:25:32: #1 tags after filtering in treatment: 3364978 INFO @ Thu, 09 Dec 2021 00:25:32: #1 Redundant rate of treatment: 0.27 INFO @ Thu, 09 Dec 2021 00:25:32: #1 finished! INFO @ Thu, 09 Dec 2021 00:25:32: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 00:25:32: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 00:25:33: #2 number of paired peaks: 3050 INFO @ Thu, 09 Dec 2021 00:25:33: start model_add_line... INFO @ Thu, 09 Dec 2021 00:25:33: start X-correlation... INFO @ Thu, 09 Dec 2021 00:25:33: end of X-cor INFO @ Thu, 09 Dec 2021 00:25:33: #2 finished! INFO @ Thu, 09 Dec 2021 00:25:33: #2 predicted fragment length is 119 bps INFO @ Thu, 09 Dec 2021 00:25:33: #2 alternative fragment length(s) may be 119 bps INFO @ Thu, 09 Dec 2021 00:25:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8845621/SRX8845621.10_model.r WARNING @ Thu, 09 Dec 2021 00:25:33: #2 Since the d (119) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 00:25:33: #2 You may need to consider one of the other alternative d(s): 119 WARNING @ Thu, 09 Dec 2021 00:25:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 00:25:33: #3 Call peaks... INFO @ Thu, 09 Dec 2021 00:25:33: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 00:25:34: 8000000 INFO @ Thu, 09 Dec 2021 00:25:43: 9000000 INFO @ Thu, 09 Dec 2021 00:25:44: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 00:25:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8845621/SRX8845621.10_peaks.xls INFO @ Thu, 09 Dec 2021 00:25:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8845621/SRX8845621.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 00:25:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8845621/SRX8845621.10_summits.bed INFO @ Thu, 09 Dec 2021 00:25:50: Done! pass1 - making usageList (6 chroms): 3 millis pass2 - checking and writing primary data (4827 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 00:25:52: 10000000 INFO @ Thu, 09 Dec 2021 00:26:02: 11000000 INFO @ Thu, 09 Dec 2021 00:26:06: #1 tag size is determined as 75 bps INFO @ Thu, 09 Dec 2021 00:26:06: #1 tag size = 75 INFO @ Thu, 09 Dec 2021 00:26:06: #1 total tags in treatment: 4625094 INFO @ Thu, 09 Dec 2021 00:26:06: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 00:26:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 00:26:06: #1 tags after filtering in treatment: 3364978 INFO @ Thu, 09 Dec 2021 00:26:06: #1 Redundant rate of treatment: 0.27 INFO @ Thu, 09 Dec 2021 00:26:06: #1 finished! INFO @ Thu, 09 Dec 2021 00:26:06: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 00:26:06: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 00:26:06: #2 number of paired peaks: 3050 INFO @ Thu, 09 Dec 2021 00:26:06: start model_add_line... INFO @ Thu, 09 Dec 2021 00:26:06: start X-correlation... INFO @ Thu, 09 Dec 2021 00:26:06: end of X-cor INFO @ Thu, 09 Dec 2021 00:26:06: #2 finished! INFO @ Thu, 09 Dec 2021 00:26:06: #2 predicted fragment length is 119 bps INFO @ Thu, 09 Dec 2021 00:26:06: #2 alternative fragment length(s) may be 119 bps INFO @ Thu, 09 Dec 2021 00:26:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8845621/SRX8845621.20_model.r WARNING @ Thu, 09 Dec 2021 00:26:06: #2 Since the d (119) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 00:26:06: #2 You may need to consider one of the other alternative d(s): 119 WARNING @ Thu, 09 Dec 2021 00:26:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 00:26:06: #3 Call peaks... INFO @ Thu, 09 Dec 2021 00:26:06: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 00:26:18: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 00:26:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8845621/SRX8845621.20_peaks.xls INFO @ Thu, 09 Dec 2021 00:26:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8845621/SRX8845621.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 00:26:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8845621/SRX8845621.20_summits.bed INFO @ Thu, 09 Dec 2021 00:26:24: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (2562 records, 4 fields): 8 millis CompletedMACS2peakCalling