Job ID = 14158894 SRX = SRX10342594 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: 00:13:36 20325733 reads; of these: 20325733 (100.00%) were paired; of these: 5410628 (26.62%) aligned concordantly 0 times 13274802 (65.31%) aligned concordantly exactly 1 time 1640303 (8.07%) aligned concordantly >1 times ---- 5410628 pairs aligned concordantly 0 times; of these: 3849444 (71.15%) aligned discordantly 1 time ---- 1561184 pairs aligned 0 times concordantly or discordantly; of these: 3122368 mates make up the pairs; of these: 1500403 (48.05%) aligned 0 times 708093 (22.68%) aligned exactly 1 time 913872 (29.27%) aligned >1 times 96.31% overall alignment rate Time searching: 00:13:36 Overall time: 00:13:36 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] 4140021 / 18756641 = 0.2207 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 18:37:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10342594/SRX10342594.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10342594/SRX10342594.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10342594/SRX10342594.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10342594/SRX10342594.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 18:37:21: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:37:21: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:37:25: 1000000 INFO @ Wed, 08 Dec 2021 18:37:29: 2000000 INFO @ Wed, 08 Dec 2021 18:37:33: 3000000 INFO @ Wed, 08 Dec 2021 18:37:37: 4000000 INFO @ Wed, 08 Dec 2021 18:37:40: 5000000 INFO @ Wed, 08 Dec 2021 18:37:44: 6000000 INFO @ Wed, 08 Dec 2021 18:37:48: 7000000 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 18:37:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10342594/SRX10342594.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10342594/SRX10342594.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10342594/SRX10342594.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10342594/SRX10342594.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 18:37:51: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:37:51: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:37:52: 8000000 INFO @ Wed, 08 Dec 2021 18:37:55: 1000000 INFO @ Wed, 08 Dec 2021 18:37:56: 9000000 INFO @ Wed, 08 Dec 2021 18:37:59: 2000000 INFO @ Wed, 08 Dec 2021 18:38:00: 10000000 INFO @ Wed, 08 Dec 2021 18:38:03: 3000000 INFO @ Wed, 08 Dec 2021 18:38:04: 11000000 INFO @ Wed, 08 Dec 2021 18:38:07: 4000000 INFO @ Wed, 08 Dec 2021 18:38:07: 12000000 INFO @ Wed, 08 Dec 2021 18:38:11: 5000000 INFO @ Wed, 08 Dec 2021 18:38:11: 13000000 INFO @ Wed, 08 Dec 2021 18:38:15: 6000000 INFO @ Wed, 08 Dec 2021 18:38:15: 14000000 INFO @ Wed, 08 Dec 2021 18:38:19: 7000000 INFO @ Wed, 08 Dec 2021 18:38:19: 15000000 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 18:38:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10342594/SRX10342594.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10342594/SRX10342594.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10342594/SRX10342594.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10342594/SRX10342594.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 18:38:21: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:38:21: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:38:23: 8000000 INFO @ Wed, 08 Dec 2021 18:38:23: 16000000 INFO @ Wed, 08 Dec 2021 18:38:26: 1000000 INFO @ Wed, 08 Dec 2021 18:38:27: 9000000 INFO @ Wed, 08 Dec 2021 18:38:27: 17000000 INFO @ Wed, 08 Dec 2021 18:38:30: 10000000 INFO @ Wed, 08 Dec 2021 18:38:31: 2000000 INFO @ Wed, 08 Dec 2021 18:38:31: 18000000 INFO @ Wed, 08 Dec 2021 18:38:34: 11000000 INFO @ Wed, 08 Dec 2021 18:38:35: 19000000 INFO @ Wed, 08 Dec 2021 18:38:36: 3000000 INFO @ Wed, 08 Dec 2021 18:38:38: 12000000 INFO @ Wed, 08 Dec 2021 18:38:39: 20000000 INFO @ Wed, 08 Dec 2021 18:38:40: 4000000 INFO @ Wed, 08 Dec 2021 18:38:42: 13000000 INFO @ Wed, 08 Dec 2021 18:38:43: 21000000 INFO @ Wed, 08 Dec 2021 18:38:45: 5000000 INFO @ Wed, 08 Dec 2021 18:38:46: 14000000 INFO @ Wed, 08 Dec 2021 18:38:47: 22000000 INFO @ Wed, 08 Dec 2021 18:38:50: 6000000 INFO @ Wed, 08 Dec 2021 18:38:50: 15000000 INFO @ Wed, 08 Dec 2021 18:38:51: 23000000 INFO @ Wed, 08 Dec 2021 18:38:54: 16000000 INFO @ Wed, 08 Dec 2021 18:38:55: 7000000 INFO @ Wed, 08 Dec 2021 18:38:55: 24000000 INFO @ Wed, 08 Dec 2021 18:38:58: 17000000 INFO @ Wed, 08 Dec 2021 18:38:59: 25000000 INFO @ Wed, 08 Dec 2021 18:38:59: 8000000 INFO @ Wed, 08 Dec 2021 18:39:02: 18000000 INFO @ Wed, 08 Dec 2021 18:39:03: 26000000 INFO @ Wed, 08 Dec 2021 18:39:04: 9000000 INFO @ Wed, 08 Dec 2021 18:39:06: 19000000 INFO @ Wed, 08 Dec 2021 18:39:07: 27000000 INFO @ Wed, 08 Dec 2021 18:39:09: 10000000 INFO @ Wed, 08 Dec 2021 18:39:10: 20000000 INFO @ Wed, 08 Dec 2021 18:39:11: 28000000 INFO @ Wed, 08 Dec 2021 18:39:14: 11000000 INFO @ Wed, 08 Dec 2021 18:39:14: 21000000 INFO @ Wed, 08 Dec 2021 18:39:15: 29000000 INFO @ Wed, 08 Dec 2021 18:39:18: 22000000 INFO @ Wed, 08 Dec 2021 18:39:19: 12000000 INFO @ Wed, 08 Dec 2021 18:39:19: 30000000 INFO @ Wed, 08 Dec 2021 18:39:22: 23000000 INFO @ Wed, 08 Dec 2021 18:39:22: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 18:39:22: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 18:39:22: #1 total tags in treatment: 11421341 INFO @ Wed, 08 Dec 2021 18:39:22: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:39:22: #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 18:39:23: #1 tags after filtering in treatment: 10567645 INFO @ Wed, 08 Dec 2021 18:39:23: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 18:39:23: #1 finished! INFO @ Wed, 08 Dec 2021 18:39:23: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:39:23: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:39:23: #2 number of paired peaks: 657 WARNING @ Wed, 08 Dec 2021 18:39:23: Fewer paired peaks (657) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 657 pairs to build model! INFO @ Wed, 08 Dec 2021 18:39:23: start model_add_line... INFO @ Wed, 08 Dec 2021 18:39:23: 13000000 INFO @ Wed, 08 Dec 2021 18:39:23: start X-correlation... INFO @ Wed, 08 Dec 2021 18:39:23: end of X-cor INFO @ Wed, 08 Dec 2021 18:39:23: #2 finished! INFO @ Wed, 08 Dec 2021 18:39:23: #2 predicted fragment length is 215 bps INFO @ Wed, 08 Dec 2021 18:39:23: #2 alternative fragment length(s) may be 4,215 bps INFO @ Wed, 08 Dec 2021 18:39:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10342594/SRX10342594.05_model.r INFO @ Wed, 08 Dec 2021 18:39:23: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:39:23: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:39:26: 24000000 INFO @ Wed, 08 Dec 2021 18:39:28: 14000000 INFO @ Wed, 08 Dec 2021 18:39:30: 25000000 INFO @ Wed, 08 Dec 2021 18:39:33: 15000000 INFO @ Wed, 08 Dec 2021 18:39:34: 26000000 INFO @ Wed, 08 Dec 2021 18:39:38: 16000000 INFO @ Wed, 08 Dec 2021 18:39:38: 27000000 INFO @ Wed, 08 Dec 2021 18:39:42: 17000000 INFO @ Wed, 08 Dec 2021 18:39:42: 28000000 INFO @ Wed, 08 Dec 2021 18:39:47: 29000000 INFO @ Wed, 08 Dec 2021 18:39:47: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:39:47: 18000000 INFO @ Wed, 08 Dec 2021 18:39:50: 30000000 INFO @ Wed, 08 Dec 2021 18:39:52: 19000000 INFO @ Wed, 08 Dec 2021 18:39:54: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 18:39:54: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 18:39:54: #1 total tags in treatment: 11421341 INFO @ Wed, 08 Dec 2021 18:39:54: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:39:54: #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 18:39:54: #1 tags after filtering in treatment: 10567645 INFO @ Wed, 08 Dec 2021 18:39:54: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 18:39:54: #1 finished! INFO @ Wed, 08 Dec 2021 18:39:54: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:39:54: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:39:55: #2 number of paired peaks: 657 WARNING @ Wed, 08 Dec 2021 18:39:55: Fewer paired peaks (657) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 657 pairs to build model! INFO @ Wed, 08 Dec 2021 18:39:55: start model_add_line... INFO @ Wed, 08 Dec 2021 18:39:55: start X-correlation... INFO @ Wed, 08 Dec 2021 18:39:55: end of X-cor INFO @ Wed, 08 Dec 2021 18:39:55: #2 finished! INFO @ Wed, 08 Dec 2021 18:39:55: #2 predicted fragment length is 215 bps INFO @ Wed, 08 Dec 2021 18:39:55: #2 alternative fragment length(s) may be 4,215 bps INFO @ Wed, 08 Dec 2021 18:39:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10342594/SRX10342594.10_model.r INFO @ Wed, 08 Dec 2021 18:39:55: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:39:55: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:39:57: 20000000 INFO @ Wed, 08 Dec 2021 18:39:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10342594/SRX10342594.05_peaks.xls INFO @ Wed, 08 Dec 2021 18:39:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10342594/SRX10342594.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:39:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10342594/SRX10342594.05_summits.bed INFO @ Wed, 08 Dec 2021 18:39:57: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5215 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:40:01: 21000000 INFO @ Wed, 08 Dec 2021 18:40:06: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 18:40:11: 23000000 INFO @ Wed, 08 Dec 2021 18:40:15: 24000000 INFO @ Wed, 08 Dec 2021 18:40:18: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:40:20: 25000000 INFO @ Wed, 08 Dec 2021 18:40:24: 26000000 INFO @ Wed, 08 Dec 2021 18:40:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10342594/SRX10342594.10_peaks.xls INFO @ Wed, 08 Dec 2021 18:40:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10342594/SRX10342594.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:40:29: 27000000 INFO @ Wed, 08 Dec 2021 18:40:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10342594/SRX10342594.10_summits.bed INFO @ Wed, 08 Dec 2021 18:40:29: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3293 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:40:34: 28000000 INFO @ Wed, 08 Dec 2021 18:40:38: 29000000 INFO @ Wed, 08 Dec 2021 18:40:43: 30000000 INFO @ Wed, 08 Dec 2021 18:40:47: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 18:40:47: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 18:40:47: #1 total tags in treatment: 11421341 INFO @ Wed, 08 Dec 2021 18:40:47: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:40:47: #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 18:40:47: #1 tags after filtering in treatment: 10567645 INFO @ Wed, 08 Dec 2021 18:40:47: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 18:40:47: #1 finished! INFO @ Wed, 08 Dec 2021 18:40:47: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:40:47: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:40:48: #2 number of paired peaks: 657 WARNING @ Wed, 08 Dec 2021 18:40:48: Fewer paired peaks (657) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 657 pairs to build model! INFO @ Wed, 08 Dec 2021 18:40:48: start model_add_line... INFO @ Wed, 08 Dec 2021 18:40:48: start X-correlation... INFO @ Wed, 08 Dec 2021 18:40:48: end of X-cor INFO @ Wed, 08 Dec 2021 18:40:48: #2 finished! INFO @ Wed, 08 Dec 2021 18:40:48: #2 predicted fragment length is 215 bps INFO @ Wed, 08 Dec 2021 18:40:48: #2 alternative fragment length(s) may be 4,215 bps INFO @ Wed, 08 Dec 2021 18:40:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10342594/SRX10342594.20_model.r INFO @ Wed, 08 Dec 2021 18:40:48: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:40:48: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 18:41:11: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:41:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10342594/SRX10342594.20_peaks.xls INFO @ Wed, 08 Dec 2021 18:41:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10342594/SRX10342594.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:41:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10342594/SRX10342594.20_summits.bed INFO @ Wed, 08 Dec 2021 18:41:21: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1192 records, 4 fields): 31 millis CompletedMACS2peakCalling