Job ID = 14159392 SRX = SRX8976740 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: 00:13:37 16836768 reads; of these: 16836768 (100.00%) were paired; of these: 1415045 (8.40%) aligned concordantly 0 times 13405761 (79.62%) aligned concordantly exactly 1 time 2015962 (11.97%) aligned concordantly >1 times ---- 1415045 pairs aligned concordantly 0 times; of these: 1020995 (72.15%) aligned discordantly 1 time ---- 394050 pairs aligned 0 times concordantly or discordantly; of these: 788100 mates make up the pairs; of these: 245414 (31.14%) aligned 0 times 256559 (32.55%) aligned exactly 1 time 286127 (36.31%) aligned >1 times 99.27% overall alignment rate Time searching: 00:13:37 Overall time: 00:13:37 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] 539888 / 16408388 = 0.0329 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 21:49:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976740/SRX8976740.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976740/SRX8976740.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976740/SRX8976740.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976740/SRX8976740.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 21:49:54: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:49:54: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:50:01: 1000000 INFO @ Wed, 08 Dec 2021 21:50:07: 2000000 INFO @ Wed, 08 Dec 2021 21:50:13: 3000000 INFO @ Wed, 08 Dec 2021 21:50:20: 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 21:50:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976740/SRX8976740.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976740/SRX8976740.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976740/SRX8976740.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976740/SRX8976740.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 21:50:24: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:50:24: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:50:26: 5000000 INFO @ Wed, 08 Dec 2021 21:50:31: 1000000 INFO @ Wed, 08 Dec 2021 21:50:33: 6000000 INFO @ Wed, 08 Dec 2021 21:50:38: 2000000 INFO @ Wed, 08 Dec 2021 21:50:40: 7000000 INFO @ Wed, 08 Dec 2021 21:50:44: 3000000 INFO @ Wed, 08 Dec 2021 21:50:47: 8000000 INFO @ Wed, 08 Dec 2021 21:50:51: 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 21:50:54: 9000000 INFO @ Wed, 08 Dec 2021 21:50:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976740/SRX8976740.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976740/SRX8976740.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976740/SRX8976740.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976740/SRX8976740.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 21:50:54: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:50:54: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:50:58: 5000000 INFO @ Wed, 08 Dec 2021 21:51:01: 10000000 INFO @ Wed, 08 Dec 2021 21:51:01: 1000000 INFO @ Wed, 08 Dec 2021 21:51:05: 6000000 INFO @ Wed, 08 Dec 2021 21:51:08: 11000000 INFO @ Wed, 08 Dec 2021 21:51:08: 2000000 INFO @ Wed, 08 Dec 2021 21:51:11: 7000000 INFO @ Wed, 08 Dec 2021 21:51:15: 12000000 INFO @ Wed, 08 Dec 2021 21:51:15: 3000000 INFO @ Wed, 08 Dec 2021 21:51:18: 8000000 INFO @ Wed, 08 Dec 2021 21:51:22: 13000000 INFO @ Wed, 08 Dec 2021 21:51:22: 4000000 INFO @ Wed, 08 Dec 2021 21:51:25: 9000000 INFO @ Wed, 08 Dec 2021 21:51:29: 14000000 INFO @ Wed, 08 Dec 2021 21:51:30: 5000000 INFO @ Wed, 08 Dec 2021 21:51:32: 10000000 INFO @ Wed, 08 Dec 2021 21:51:36: 15000000 INFO @ Wed, 08 Dec 2021 21:51:37: 6000000 INFO @ Wed, 08 Dec 2021 21:51:38: 11000000 INFO @ Wed, 08 Dec 2021 21:51:43: 16000000 INFO @ Wed, 08 Dec 2021 21:51:44: 7000000 INFO @ Wed, 08 Dec 2021 21:51:45: 12000000 INFO @ Wed, 08 Dec 2021 21:51:50: 17000000 INFO @ Wed, 08 Dec 2021 21:51:52: 8000000 INFO @ Wed, 08 Dec 2021 21:51:52: 13000000 INFO @ Wed, 08 Dec 2021 21:51:57: 18000000 INFO @ Wed, 08 Dec 2021 21:51:59: 14000000 INFO @ Wed, 08 Dec 2021 21:51:59: 9000000 INFO @ Wed, 08 Dec 2021 21:52:04: 19000000 INFO @ Wed, 08 Dec 2021 21:52:06: 15000000 INFO @ Wed, 08 Dec 2021 21:52:06: 10000000 INFO @ Wed, 08 Dec 2021 21:52:11: 20000000 INFO @ Wed, 08 Dec 2021 21:52:12: 16000000 INFO @ Wed, 08 Dec 2021 21:52:13: 11000000 INFO @ Wed, 08 Dec 2021 21:52:19: 21000000 INFO @ Wed, 08 Dec 2021 21:52:19: 17000000 INFO @ Wed, 08 Dec 2021 21:52:21: 12000000 INFO @ Wed, 08 Dec 2021 21:52:26: 22000000 INFO @ Wed, 08 Dec 2021 21:52:26: 18000000 INFO @ Wed, 08 Dec 2021 21:52:28: 13000000 INFO @ Wed, 08 Dec 2021 21:52:33: 19000000 INFO @ Wed, 08 Dec 2021 21:52:33: 23000000 INFO @ Wed, 08 Dec 2021 21:52:35: 14000000 INFO @ Wed, 08 Dec 2021 21:52:39: 20000000 INFO @ Wed, 08 Dec 2021 21:52:40: 24000000 INFO @ Wed, 08 Dec 2021 21:52:42: 15000000 INFO @ Wed, 08 Dec 2021 21:52:46: 21000000 INFO @ Wed, 08 Dec 2021 21:52:47: 25000000 INFO @ Wed, 08 Dec 2021 21:52:49: 16000000 INFO @ Wed, 08 Dec 2021 21:52:53: 22000000 INFO @ Wed, 08 Dec 2021 21:52:54: 26000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 21:52:56: 17000000 INFO @ Wed, 08 Dec 2021 21:53:00: 23000000 INFO @ Wed, 08 Dec 2021 21:53:01: 27000000 INFO @ Wed, 08 Dec 2021 21:53:03: 18000000 INFO @ Wed, 08 Dec 2021 21:53:06: 24000000 INFO @ Wed, 08 Dec 2021 21:53:08: 28000000 INFO @ Wed, 08 Dec 2021 21:53:11: 19000000 INFO @ Wed, 08 Dec 2021 21:53:13: 25000000 INFO @ Wed, 08 Dec 2021 21:53:16: 29000000 INFO @ Wed, 08 Dec 2021 21:53:18: 20000000 INFO @ Wed, 08 Dec 2021 21:53:20: 26000000 INFO @ Wed, 08 Dec 2021 21:53:23: 30000000 INFO @ Wed, 08 Dec 2021 21:53:25: 21000000 INFO @ Wed, 08 Dec 2021 21:53:27: 27000000 INFO @ Wed, 08 Dec 2021 21:53:30: 31000000 INFO @ Wed, 08 Dec 2021 21:53:32: 22000000 INFO @ Wed, 08 Dec 2021 21:53:34: 28000000 INFO @ Wed, 08 Dec 2021 21:53:37: 32000000 INFO @ Wed, 08 Dec 2021 21:53:39: 23000000 INFO @ Wed, 08 Dec 2021 21:53:40: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 21:53:40: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 21:53:40: #1 total tags in treatment: 14906079 INFO @ Wed, 08 Dec 2021 21:53:40: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:53:40: #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 21:53:40: #1 tags after filtering in treatment: 13746502 INFO @ Wed, 08 Dec 2021 21:53:40: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 21:53:40: #1 finished! INFO @ Wed, 08 Dec 2021 21:53:40: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:53:40: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:53:40: 29000000 INFO @ Wed, 08 Dec 2021 21:53:41: #2 number of paired peaks: 321 WARNING @ Wed, 08 Dec 2021 21:53:41: Fewer paired peaks (321) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 321 pairs to build model! INFO @ Wed, 08 Dec 2021 21:53:41: start model_add_line... INFO @ Wed, 08 Dec 2021 21:53:41: start X-correlation... INFO @ Wed, 08 Dec 2021 21:53:41: end of X-cor INFO @ Wed, 08 Dec 2021 21:53:41: #2 finished! INFO @ Wed, 08 Dec 2021 21:53:41: #2 predicted fragment length is 128 bps INFO @ Wed, 08 Dec 2021 21:53:41: #2 alternative fragment length(s) may be 4,128 bps INFO @ Wed, 08 Dec 2021 21:53:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976740/SRX8976740.05_model.r INFO @ Wed, 08 Dec 2021 21:53:41: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:53:41: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 21:53:46: 24000000 INFO @ Wed, 08 Dec 2021 21:53:47: 30000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 21:53:54: 25000000 INFO @ Wed, 08 Dec 2021 21:53:54: 31000000 INFO @ Wed, 08 Dec 2021 21:54:00: 32000000 INFO @ Wed, 08 Dec 2021 21:54:01: 26000000 INFO @ Wed, 08 Dec 2021 21:54:02: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 21:54:02: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 21:54:02: #1 total tags in treatment: 14906079 INFO @ Wed, 08 Dec 2021 21:54:02: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:54:02: #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 21:54:03: #1 tags after filtering in treatment: 13746502 INFO @ Wed, 08 Dec 2021 21:54:03: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 21:54:03: #1 finished! INFO @ Wed, 08 Dec 2021 21:54:03: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:54:03: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:54:04: #2 number of paired peaks: 321 WARNING @ Wed, 08 Dec 2021 21:54:04: Fewer paired peaks (321) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 321 pairs to build model! INFO @ Wed, 08 Dec 2021 21:54:04: start model_add_line... INFO @ Wed, 08 Dec 2021 21:54:04: start X-correlation... INFO @ Wed, 08 Dec 2021 21:54:04: end of X-cor INFO @ Wed, 08 Dec 2021 21:54:04: #2 finished! INFO @ Wed, 08 Dec 2021 21:54:04: #2 predicted fragment length is 128 bps INFO @ Wed, 08 Dec 2021 21:54:04: #2 alternative fragment length(s) may be 4,128 bps INFO @ Wed, 08 Dec 2021 21:54:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976740/SRX8976740.10_model.r INFO @ Wed, 08 Dec 2021 21:54:04: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:54:04: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 21:54:07: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:54:07: 27000000 INFO @ Wed, 08 Dec 2021 21:54:13: 28000000 INFO @ Wed, 08 Dec 2021 21:54:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976740/SRX8976740.05_peaks.xls INFO @ Wed, 08 Dec 2021 21:54:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976740/SRX8976740.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:54:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976740/SRX8976740.05_summits.bed INFO @ Wed, 08 Dec 2021 21:54:19: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (370 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 21:54:20: 29000000 INFO @ Wed, 08 Dec 2021 21:54:26: 30000000 INFO @ Wed, 08 Dec 2021 21:54:29: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:54:32: 31000000 INFO @ Wed, 08 Dec 2021 21:54:38: 32000000 INFO @ Wed, 08 Dec 2021 21:54:40: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 21:54:40: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 21:54:40: #1 total tags in treatment: 14906079 INFO @ Wed, 08 Dec 2021 21:54:40: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:54:40: #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 21:54:41: #1 tags after filtering in treatment: 13746502 INFO @ Wed, 08 Dec 2021 21:54:41: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 21:54:41: #1 finished! INFO @ Wed, 08 Dec 2021 21:54:41: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:54:41: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:54:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976740/SRX8976740.10_peaks.xls INFO @ Wed, 08 Dec 2021 21:54:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976740/SRX8976740.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:54:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976740/SRX8976740.10_summits.bed INFO @ Wed, 08 Dec 2021 21:54:41: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (272 records, 4 fields): 125 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 21:54:42: #2 number of paired peaks: 321 WARNING @ Wed, 08 Dec 2021 21:54:42: Fewer paired peaks (321) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 321 pairs to build model! INFO @ Wed, 08 Dec 2021 21:54:42: start model_add_line... INFO @ Wed, 08 Dec 2021 21:54:42: start X-correlation... INFO @ Wed, 08 Dec 2021 21:54:42: end of X-cor INFO @ Wed, 08 Dec 2021 21:54:42: #2 finished! INFO @ Wed, 08 Dec 2021 21:54:42: #2 predicted fragment length is 128 bps INFO @ Wed, 08 Dec 2021 21:54:42: #2 alternative fragment length(s) may be 4,128 bps INFO @ Wed, 08 Dec 2021 21:54:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976740/SRX8976740.20_model.r INFO @ Wed, 08 Dec 2021 21:54:42: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:54:42: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 21:55:06: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:55:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976740/SRX8976740.20_peaks.xls INFO @ Wed, 08 Dec 2021 21:55:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976740/SRX8976740.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:55:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976740/SRX8976740.20_summits.bed INFO @ Wed, 08 Dec 2021 21:55:18: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (181 records, 4 fields): 1 millis CompletedMACS2peakCalling