Job ID = 14158390 SRX = SRX10641184 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 20924703 spots for SRR14280094/SRR14280094.sra Written 20924703 spots for SRR14280094/SRR14280094.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159057 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:22:25 20924703 reads; of these: 20924703 (100.00%) were paired; of these: 14722859 (70.36%) aligned concordantly 0 times 5329735 (25.47%) aligned concordantly exactly 1 time 872109 (4.17%) aligned concordantly >1 times ---- 14722859 pairs aligned concordantly 0 times; of these: 3037240 (20.63%) aligned discordantly 1 time ---- 11685619 pairs aligned 0 times concordantly or discordantly; of these: 23371238 mates make up the pairs; of these: 21873821 (93.59%) aligned 0 times 814636 (3.49%) aligned exactly 1 time 682781 (2.92%) aligned >1 times 47.73% overall alignment rate Time searching: 00:22:25 Overall time: 00:22:25 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 16 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] 1162785 / 9217477 = 0.1262 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 @ Wed, 08 Dec 2021 17:38:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641184/SRX10641184.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641184/SRX10641184.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641184/SRX10641184.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641184/SRX10641184.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 @ Wed, 08 Dec 2021 17:38:18: #1 read tag files... INFO @ Wed, 08 Dec 2021 17:38:18: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 17:38:25: 1000000 INFO @ Wed, 08 Dec 2021 17:38:33: 2000000 INFO @ Wed, 08 Dec 2021 17:38:40: 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 @ Wed, 08 Dec 2021 17:38:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641184/SRX10641184.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641184/SRX10641184.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641184/SRX10641184.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641184/SRX10641184.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 @ Wed, 08 Dec 2021 17:38:47: #1 read tag files... INFO @ Wed, 08 Dec 2021 17:38:47: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 17:38:49: 4000000 INFO @ Wed, 08 Dec 2021 17:38:56: 1000000 INFO @ Wed, 08 Dec 2021 17:38:57: 5000000 INFO @ Wed, 08 Dec 2021 17:39:05: 2000000 INFO @ Wed, 08 Dec 2021 17:39:06: 6000000 INFO @ Wed, 08 Dec 2021 17:39:13: 3000000 INFO @ Wed, 08 Dec 2021 17:39:15: 7000000 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 @ Wed, 08 Dec 2021 17:39:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641184/SRX10641184.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641184/SRX10641184.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641184/SRX10641184.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641184/SRX10641184.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 @ Wed, 08 Dec 2021 17:39:17: #1 read tag files... INFO @ Wed, 08 Dec 2021 17:39:17: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 17:39:22: 4000000 INFO @ Wed, 08 Dec 2021 17:39:23: 8000000 INFO @ Wed, 08 Dec 2021 17:39:26: 1000000 INFO @ Wed, 08 Dec 2021 17:39:31: 5000000 INFO @ Wed, 08 Dec 2021 17:39:32: 9000000 INFO @ Wed, 08 Dec 2021 17:39:35: 2000000 INFO @ Wed, 08 Dec 2021 17:39:40: 6000000 INFO @ Wed, 08 Dec 2021 17:39:41: 10000000 INFO @ Wed, 08 Dec 2021 17:39:43: 3000000 INFO @ Wed, 08 Dec 2021 17:39:49: 7000000 INFO @ Wed, 08 Dec 2021 17:39:50: 11000000 INFO @ Wed, 08 Dec 2021 17:39:53: 4000000 INFO @ Wed, 08 Dec 2021 17:39:57: 8000000 INFO @ Wed, 08 Dec 2021 17:39:59: 12000000 INFO @ Wed, 08 Dec 2021 17:40:02: 5000000 INFO @ Wed, 08 Dec 2021 17:40:06: 9000000 INFO @ Wed, 08 Dec 2021 17:40:08: 13000000 INFO @ Wed, 08 Dec 2021 17:40:10: 6000000 INFO @ Wed, 08 Dec 2021 17:40:15: 10000000 INFO @ Wed, 08 Dec 2021 17:40:17: 14000000 INFO @ Wed, 08 Dec 2021 17:40:19: 7000000 INFO @ Wed, 08 Dec 2021 17:40:24: 11000000 INFO @ Wed, 08 Dec 2021 17:40:26: 15000000 INFO @ Wed, 08 Dec 2021 17:40:28: 8000000 INFO @ Wed, 08 Dec 2021 17:40:34: 12000000 INFO @ Wed, 08 Dec 2021 17:40:36: 16000000 INFO @ Wed, 08 Dec 2021 17:40:37: 9000000 INFO @ Wed, 08 Dec 2021 17:40:43: 13000000 INFO @ Wed, 08 Dec 2021 17:40:45: 10000000 INFO @ Wed, 08 Dec 2021 17:40:46: 17000000 INFO @ Wed, 08 Dec 2021 17:40:51: 14000000 INFO @ Wed, 08 Dec 2021 17:40:52: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 17:40:52: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 17:40:52: #1 total tags in treatment: 5335182 INFO @ Wed, 08 Dec 2021 17:40:52: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 17:40:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 17:40:52: #1 tags after filtering in treatment: 4925165 INFO @ Wed, 08 Dec 2021 17:40:52: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 17:40:52: #1 finished! INFO @ Wed, 08 Dec 2021 17:40:52: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 17:40:52: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 17:40:53: #2 number of paired peaks: 1308 INFO @ Wed, 08 Dec 2021 17:40:53: start model_add_line... INFO @ Wed, 08 Dec 2021 17:40:53: start X-correlation... INFO @ Wed, 08 Dec 2021 17:40:53: end of X-cor INFO @ Wed, 08 Dec 2021 17:40:53: #2 finished! INFO @ Wed, 08 Dec 2021 17:40:53: #2 predicted fragment length is 240 bps INFO @ Wed, 08 Dec 2021 17:40:53: #2 alternative fragment length(s) may be 4,238,240 bps INFO @ Wed, 08 Dec 2021 17:40:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641184/SRX10641184.05_model.r WARNING @ Wed, 08 Dec 2021 17:40:53: #2 Since the d (240) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 17:40:53: #2 You may need to consider one of the other alternative d(s): 4,238,240 WARNING @ Wed, 08 Dec 2021 17:40:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 17:40:53: #3 Call peaks... INFO @ Wed, 08 Dec 2021 17:40:53: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 17:40:55: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 17:41:01: 15000000 INFO @ Wed, 08 Dec 2021 17:41:04: 12000000 INFO @ Wed, 08 Dec 2021 17:41:06: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 17:41:10: 16000000 INFO @ Wed, 08 Dec 2021 17:41:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641184/SRX10641184.05_peaks.xls INFO @ Wed, 08 Dec 2021 17:41:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641184/SRX10641184.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 17:41:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641184/SRX10641184.05_summits.bed INFO @ Wed, 08 Dec 2021 17:41:11: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1055 records, 4 fields): 233 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 17:41:13: 13000000 INFO @ Wed, 08 Dec 2021 17:41:20: 17000000 INFO @ Wed, 08 Dec 2021 17:41:21: 14000000 INFO @ Wed, 08 Dec 2021 17:41:26: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 17:41:26: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 17:41:26: #1 total tags in treatment: 5335182 INFO @ Wed, 08 Dec 2021 17:41:26: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 17:41:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 17:41:26: #1 tags after filtering in treatment: 4925165 INFO @ Wed, 08 Dec 2021 17:41:26: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 17:41:26: #1 finished! INFO @ Wed, 08 Dec 2021 17:41:26: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 17:41:26: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 17:41:27: #2 number of paired peaks: 1308 INFO @ Wed, 08 Dec 2021 17:41:27: start model_add_line... INFO @ Wed, 08 Dec 2021 17:41:27: start X-correlation... INFO @ Wed, 08 Dec 2021 17:41:27: end of X-cor INFO @ Wed, 08 Dec 2021 17:41:27: #2 finished! INFO @ Wed, 08 Dec 2021 17:41:27: #2 predicted fragment length is 240 bps INFO @ Wed, 08 Dec 2021 17:41:27: #2 alternative fragment length(s) may be 4,238,240 bps INFO @ Wed, 08 Dec 2021 17:41:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641184/SRX10641184.10_model.r WARNING @ Wed, 08 Dec 2021 17:41:27: #2 Since the d (240) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 17:41:27: #2 You may need to consider one of the other alternative d(s): 4,238,240 WARNING @ Wed, 08 Dec 2021 17:41:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 17:41:27: #3 Call peaks... INFO @ Wed, 08 Dec 2021 17:41:27: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 17:41:30: 15000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 17:41:39: 16000000 INFO @ Wed, 08 Dec 2021 17:41:40: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 17:41:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641184/SRX10641184.10_peaks.xls INFO @ Wed, 08 Dec 2021 17:41:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641184/SRX10641184.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 17:41:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641184/SRX10641184.10_summits.bed INFO @ Wed, 08 Dec 2021 17:41:46: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (527 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 17:41:48: 17000000 INFO @ Wed, 08 Dec 2021 17:41:54: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 17:41:54: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 17:41:54: #1 total tags in treatment: 5335182 INFO @ Wed, 08 Dec 2021 17:41:54: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 17:41:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 17:41:54: #1 tags after filtering in treatment: 4925165 INFO @ Wed, 08 Dec 2021 17:41:54: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 17:41:54: #1 finished! INFO @ Wed, 08 Dec 2021 17:41:54: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 17:41:54: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 17:41:54: #2 number of paired peaks: 1308 INFO @ Wed, 08 Dec 2021 17:41:54: start model_add_line... INFO @ Wed, 08 Dec 2021 17:41:54: start X-correlation... INFO @ Wed, 08 Dec 2021 17:41:54: end of X-cor INFO @ Wed, 08 Dec 2021 17:41:54: #2 finished! INFO @ Wed, 08 Dec 2021 17:41:54: #2 predicted fragment length is 240 bps INFO @ Wed, 08 Dec 2021 17:41:54: #2 alternative fragment length(s) may be 4,238,240 bps INFO @ Wed, 08 Dec 2021 17:41:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641184/SRX10641184.20_model.r WARNING @ Wed, 08 Dec 2021 17:41:54: #2 Since the d (240) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 17:41:54: #2 You may need to consider one of the other alternative d(s): 4,238,240 WARNING @ Wed, 08 Dec 2021 17:41:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 17:41:54: #3 Call peaks... INFO @ Wed, 08 Dec 2021 17:41:54: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 17:42:07: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 17:42:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641184/SRX10641184.20_peaks.xls INFO @ Wed, 08 Dec 2021 17:42:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641184/SRX10641184.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 17:42:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641184/SRX10641184.20_summits.bed INFO @ Wed, 08 Dec 2021 17:42:13: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (306 records, 4 fields): 1 millis CompletedMACS2peakCalling