Job ID = 14159319 SRX = SRX8976728 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: 00:11:41 15653750 reads; of these: 15653750 (100.00%) were paired; of these: 447131 (2.86%) aligned concordantly 0 times 13210348 (84.39%) aligned concordantly exactly 1 time 1996271 (12.75%) aligned concordantly >1 times ---- 447131 pairs aligned concordantly 0 times; of these: 237545 (53.13%) aligned discordantly 1 time ---- 209586 pairs aligned 0 times concordantly or discordantly; of these: 419172 mates make up the pairs; of these: 197613 (47.14%) aligned 0 times 126992 (30.30%) aligned exactly 1 time 94567 (22.56%) aligned >1 times 99.37% overall alignment rate Time searching: 00:11:41 Overall time: 00:11:41 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] 445100 / 15409106 = 0.0289 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 21:13:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976728/SRX8976728.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976728/SRX8976728.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976728/SRX8976728.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976728/SRX8976728.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 21:13:00: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:13:00: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:13:06: 1000000 INFO @ Wed, 08 Dec 2021 21:13:11: 2000000 INFO @ Wed, 08 Dec 2021 21:13:17: 3000000 INFO @ Wed, 08 Dec 2021 21:13:22: 4000000 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 21:13:28: 5000000 INFO @ Wed, 08 Dec 2021 21:13:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976728/SRX8976728.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976728/SRX8976728.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976728/SRX8976728.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976728/SRX8976728.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 21:13:30: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:13:30: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:13:33: 6000000 INFO @ Wed, 08 Dec 2021 21:13:36: 1000000 INFO @ Wed, 08 Dec 2021 21:13:40: 7000000 INFO @ Wed, 08 Dec 2021 21:13:42: 2000000 INFO @ Wed, 08 Dec 2021 21:13:46: 8000000 INFO @ Wed, 08 Dec 2021 21:13:48: 3000000 INFO @ Wed, 08 Dec 2021 21:13:52: 9000000 INFO @ Wed, 08 Dec 2021 21:13:53: 4000000 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 21:13:58: 10000000 INFO @ Wed, 08 Dec 2021 21:13:59: 5000000 INFO @ Wed, 08 Dec 2021 21:13:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976728/SRX8976728.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976728/SRX8976728.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976728/SRX8976728.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976728/SRX8976728.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 21:13:59: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:13:59: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:14:04: 11000000 INFO @ Wed, 08 Dec 2021 21:14:05: 6000000 INFO @ Wed, 08 Dec 2021 21:14:06: 1000000 INFO @ Wed, 08 Dec 2021 21:14:10: 12000000 INFO @ Wed, 08 Dec 2021 21:14:11: 7000000 INFO @ Wed, 08 Dec 2021 21:14:12: 2000000 INFO @ Wed, 08 Dec 2021 21:14:16: 13000000 INFO @ Wed, 08 Dec 2021 21:14:17: 8000000 INFO @ Wed, 08 Dec 2021 21:14:17: 3000000 INFO @ Wed, 08 Dec 2021 21:14:22: 14000000 INFO @ Wed, 08 Dec 2021 21:14:23: 9000000 INFO @ Wed, 08 Dec 2021 21:14:23: 4000000 INFO @ Wed, 08 Dec 2021 21:14:28: 15000000 INFO @ Wed, 08 Dec 2021 21:14:28: 10000000 INFO @ Wed, 08 Dec 2021 21:14:29: 5000000 INFO @ Wed, 08 Dec 2021 21:14:34: 16000000 INFO @ Wed, 08 Dec 2021 21:14:34: 11000000 INFO @ Wed, 08 Dec 2021 21:14:35: 6000000 INFO @ Wed, 08 Dec 2021 21:14:40: 17000000 INFO @ Wed, 08 Dec 2021 21:14:40: 12000000 INFO @ Wed, 08 Dec 2021 21:14:41: 7000000 INFO @ Wed, 08 Dec 2021 21:14:46: 18000000 INFO @ Wed, 08 Dec 2021 21:14:46: 13000000 INFO @ Wed, 08 Dec 2021 21:14:47: 8000000 INFO @ Wed, 08 Dec 2021 21:14:52: 14000000 INFO @ Wed, 08 Dec 2021 21:14:52: 19000000 INFO @ Wed, 08 Dec 2021 21:14:52: 9000000 INFO @ Wed, 08 Dec 2021 21:14:57: 15000000 INFO @ Wed, 08 Dec 2021 21:14:58: 20000000 INFO @ Wed, 08 Dec 2021 21:14:58: 10000000 INFO @ Wed, 08 Dec 2021 21:15:03: 16000000 INFO @ Wed, 08 Dec 2021 21:15:04: 21000000 INFO @ Wed, 08 Dec 2021 21:15:04: 11000000 INFO @ Wed, 08 Dec 2021 21:15:09: 17000000 INFO @ Wed, 08 Dec 2021 21:15:10: 22000000 INFO @ Wed, 08 Dec 2021 21:15:10: 12000000 INFO @ Wed, 08 Dec 2021 21:15:15: 18000000 INFO @ Wed, 08 Dec 2021 21:15:15: 13000000 INFO @ Wed, 08 Dec 2021 21:15:15: 23000000 INFO @ Wed, 08 Dec 2021 21:15:20: 19000000 INFO @ Wed, 08 Dec 2021 21:15:21: 14000000 INFO @ Wed, 08 Dec 2021 21:15:21: 24000000 INFO @ Wed, 08 Dec 2021 21:15:26: 20000000 INFO @ Wed, 08 Dec 2021 21:15:27: 15000000 INFO @ Wed, 08 Dec 2021 21:15:28: 25000000 INFO @ Wed, 08 Dec 2021 21:15:32: 21000000 INFO @ Wed, 08 Dec 2021 21:15:33: 16000000 INFO @ Wed, 08 Dec 2021 21:15:34: 26000000 INFO @ Wed, 08 Dec 2021 21:15:38: 22000000 INFO @ Wed, 08 Dec 2021 21:15:38: 17000000 INFO @ Wed, 08 Dec 2021 21:15:40: 27000000 INFO @ Wed, 08 Dec 2021 21:15:43: 23000000 INFO @ Wed, 08 Dec 2021 21:15:44: 18000000 INFO @ Wed, 08 Dec 2021 21:15:46: 28000000 INFO @ Wed, 08 Dec 2021 21:15:49: 24000000 INFO @ Wed, 08 Dec 2021 21:15:50: 19000000 INFO @ Wed, 08 Dec 2021 21:15:52: 29000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 21:15:55: 25000000 INFO @ Wed, 08 Dec 2021 21:15:55: 20000000 INFO @ Wed, 08 Dec 2021 21:15:58: 30000000 INFO @ Wed, 08 Dec 2021 21:15:59: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 21:15:59: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 21:15:59: #1 total tags in treatment: 14765172 INFO @ Wed, 08 Dec 2021 21:15:59: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:15:59: #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 21:16:00: #1 tags after filtering in treatment: 13673940 INFO @ Wed, 08 Dec 2021 21:16:00: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 21:16:00: #1 finished! INFO @ Wed, 08 Dec 2021 21:16:00: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:16:00: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:16:00: 26000000 INFO @ Wed, 08 Dec 2021 21:16:01: #2 number of paired peaks: 304 WARNING @ Wed, 08 Dec 2021 21:16:01: Fewer paired peaks (304) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 304 pairs to build model! INFO @ Wed, 08 Dec 2021 21:16:01: start model_add_line... INFO @ Wed, 08 Dec 2021 21:16:01: start X-correlation... INFO @ Wed, 08 Dec 2021 21:16:01: end of X-cor INFO @ Wed, 08 Dec 2021 21:16:01: #2 finished! INFO @ Wed, 08 Dec 2021 21:16:01: #2 predicted fragment length is 129 bps INFO @ Wed, 08 Dec 2021 21:16:01: #2 alternative fragment length(s) may be 4,129 bps INFO @ Wed, 08 Dec 2021 21:16:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976728/SRX8976728.05_model.r INFO @ Wed, 08 Dec 2021 21:16:01: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:16:01: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 21:16:01: 21000000 INFO @ Wed, 08 Dec 2021 21:16:06: 27000000 INFO @ Wed, 08 Dec 2021 21:16:06: 22000000 INFO @ Wed, 08 Dec 2021 21:16:12: 28000000 INFO @ Wed, 08 Dec 2021 21:16:12: 23000000 INFO @ Wed, 08 Dec 2021 21:16:17: 29000000 INFO @ Wed, 08 Dec 2021 21:16:17: 24000000 INFO @ Wed, 08 Dec 2021 21:16:22: 30000000 INFO @ Wed, 08 Dec 2021 21:16:23: 25000000 INFO @ Wed, 08 Dec 2021 21:16:24: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 21:16:24: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 21:16:24: #1 total tags in treatment: 14765172 INFO @ Wed, 08 Dec 2021 21:16:24: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:16:24: #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 21:16:24: #1 tags after filtering in treatment: 13673940 INFO @ Wed, 08 Dec 2021 21:16:24: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 21:16:24: #1 finished! INFO @ Wed, 08 Dec 2021 21:16:24: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:16:24: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:16:25: #2 number of paired peaks: 304 WARNING @ Wed, 08 Dec 2021 21:16:25: Fewer paired peaks (304) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 304 pairs to build model! INFO @ Wed, 08 Dec 2021 21:16:25: start model_add_line... INFO @ Wed, 08 Dec 2021 21:16:25: start X-correlation... INFO @ Wed, 08 Dec 2021 21:16:25: end of X-cor INFO @ Wed, 08 Dec 2021 21:16:25: #2 finished! INFO @ Wed, 08 Dec 2021 21:16:25: #2 predicted fragment length is 129 bps INFO @ Wed, 08 Dec 2021 21:16:25: #2 alternative fragment length(s) may be 4,129 bps INFO @ Wed, 08 Dec 2021 21:16:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976728/SRX8976728.10_model.r INFO @ Wed, 08 Dec 2021 21:16:25: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:16:25: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 21:16:25: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:16:28: 26000000 INFO @ Wed, 08 Dec 2021 21:16:33: 27000000 INFO @ Wed, 08 Dec 2021 21:16:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976728/SRX8976728.05_peaks.xls INFO @ Wed, 08 Dec 2021 21:16:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976728/SRX8976728.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:16:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976728/SRX8976728.05_summits.bed INFO @ Wed, 08 Dec 2021 21:16:37: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (366 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 21:16:37: 28000000 INFO @ Wed, 08 Dec 2021 21:16:42: 29000000 INFO @ Wed, 08 Dec 2021 21:16:46: 30000000 INFO @ Wed, 08 Dec 2021 21:16:47: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 21:16:47: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 21:16:47: #1 total tags in treatment: 14765172 INFO @ Wed, 08 Dec 2021 21:16:47: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:16:47: #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 21:16:48: #1 tags after filtering in treatment: 13673940 INFO @ Wed, 08 Dec 2021 21:16:48: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 21:16:48: #1 finished! INFO @ Wed, 08 Dec 2021 21:16:48: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:16:48: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:16:49: #2 number of paired peaks: 304 WARNING @ Wed, 08 Dec 2021 21:16:49: Fewer paired peaks (304) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 304 pairs to build model! INFO @ Wed, 08 Dec 2021 21:16:49: start model_add_line... INFO @ Wed, 08 Dec 2021 21:16:49: start X-correlation... INFO @ Wed, 08 Dec 2021 21:16:49: end of X-cor INFO @ Wed, 08 Dec 2021 21:16:49: #2 finished! INFO @ Wed, 08 Dec 2021 21:16:49: #2 predicted fragment length is 129 bps INFO @ Wed, 08 Dec 2021 21:16:49: #2 alternative fragment length(s) may be 4,129 bps INFO @ Wed, 08 Dec 2021 21:16:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976728/SRX8976728.20_model.r INFO @ Wed, 08 Dec 2021 21:16:49: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:16:49: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 21:16:51: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:17:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976728/SRX8976728.10_peaks.xls INFO @ Wed, 08 Dec 2021 21:17:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976728/SRX8976728.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:17:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976728/SRX8976728.10_summits.bed INFO @ Wed, 08 Dec 2021 21:17:03: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (275 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 21:17:14: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:17:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976728/SRX8976728.20_peaks.xls INFO @ Wed, 08 Dec 2021 21:17:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976728/SRX8976728.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:17:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976728/SRX8976728.20_summits.bed INFO @ Wed, 08 Dec 2021 21:17:26: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (168 records, 4 fields): 1 millis CompletedMACS2peakCalling