Job ID = 14160471 SRX = SRX9555458 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: 00:16:37 20336473 reads; of these: 20336473 (100.00%) were paired; of these: 1977434 (9.72%) aligned concordantly 0 times 15902776 (78.20%) aligned concordantly exactly 1 time 2456263 (12.08%) aligned concordantly >1 times ---- 1977434 pairs aligned concordantly 0 times; of these: 864563 (43.72%) aligned discordantly 1 time ---- 1112871 pairs aligned 0 times concordantly or discordantly; of these: 2225742 mates make up the pairs; of these: 1469739 (66.03%) aligned 0 times 501944 (22.55%) aligned exactly 1 time 254059 (11.41%) aligned >1 times 96.39% overall alignment rate Time searching: 00:16:37 Overall time: 00:16:37 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 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] 2086229 / 19211966 = 0.1086 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 03:07:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9555458/SRX9555458.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9555458/SRX9555458.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9555458/SRX9555458.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9555458/SRX9555458.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 03:07:09: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:07:09: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:07:14: 1000000 INFO @ Thu, 09 Dec 2021 03:07:19: 2000000 INFO @ Thu, 09 Dec 2021 03:07:24: 3000000 INFO @ Thu, 09 Dec 2021 03:07:29: 4000000 INFO @ Thu, 09 Dec 2021 03:07:34: 5000000 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 03:07:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9555458/SRX9555458.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9555458/SRX9555458.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9555458/SRX9555458.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9555458/SRX9555458.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 03:07:39: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:07:39: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:07:39: 6000000 INFO @ Thu, 09 Dec 2021 03:07:44: 1000000 INFO @ Thu, 09 Dec 2021 03:07:45: 7000000 INFO @ Thu, 09 Dec 2021 03:07:50: 2000000 INFO @ Thu, 09 Dec 2021 03:07:50: 8000000 INFO @ Thu, 09 Dec 2021 03:07:56: 3000000 INFO @ Thu, 09 Dec 2021 03:07:56: 9000000 INFO @ Thu, 09 Dec 2021 03:08:01: 4000000 INFO @ Thu, 09 Dec 2021 03:08:02: 10000000 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 03:08:07: 5000000 INFO @ Thu, 09 Dec 2021 03:08:07: 11000000 INFO @ Thu, 09 Dec 2021 03:08:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9555458/SRX9555458.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9555458/SRX9555458.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9555458/SRX9555458.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9555458/SRX9555458.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 03:08:09: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:08:09: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:08:13: 6000000 INFO @ Thu, 09 Dec 2021 03:08:13: 12000000 INFO @ Thu, 09 Dec 2021 03:08:15: 1000000 INFO @ Thu, 09 Dec 2021 03:08:19: 7000000 INFO @ Thu, 09 Dec 2021 03:08:19: 13000000 INFO @ Thu, 09 Dec 2021 03:08:20: 2000000 INFO @ Thu, 09 Dec 2021 03:08:24: 8000000 INFO @ Thu, 09 Dec 2021 03:08:25: 14000000 INFO @ Thu, 09 Dec 2021 03:08:26: 3000000 INFO @ Thu, 09 Dec 2021 03:08:30: 9000000 INFO @ Thu, 09 Dec 2021 03:08:30: 15000000 INFO @ Thu, 09 Dec 2021 03:08:32: 4000000 INFO @ Thu, 09 Dec 2021 03:08:36: 10000000 INFO @ Thu, 09 Dec 2021 03:08:36: 16000000 INFO @ Thu, 09 Dec 2021 03:08:38: 5000000 INFO @ Thu, 09 Dec 2021 03:08:42: 11000000 INFO @ Thu, 09 Dec 2021 03:08:42: 17000000 INFO @ Thu, 09 Dec 2021 03:08:44: 6000000 INFO @ Thu, 09 Dec 2021 03:08:48: 12000000 INFO @ Thu, 09 Dec 2021 03:08:48: 18000000 INFO @ Thu, 09 Dec 2021 03:08:50: 7000000 INFO @ Thu, 09 Dec 2021 03:08:54: 13000000 INFO @ Thu, 09 Dec 2021 03:08:54: 19000000 INFO @ Thu, 09 Dec 2021 03:08:56: 8000000 INFO @ Thu, 09 Dec 2021 03:08:59: 14000000 INFO @ Thu, 09 Dec 2021 03:08:59: 20000000 INFO @ Thu, 09 Dec 2021 03:09:02: 9000000 INFO @ Thu, 09 Dec 2021 03:09:05: 21000000 INFO @ Thu, 09 Dec 2021 03:09:05: 15000000 INFO @ Thu, 09 Dec 2021 03:09:08: 10000000 INFO @ Thu, 09 Dec 2021 03:09:11: 22000000 INFO @ Thu, 09 Dec 2021 03:09:11: 16000000 INFO @ Thu, 09 Dec 2021 03:09:13: 11000000 INFO @ Thu, 09 Dec 2021 03:09:17: 23000000 INFO @ Thu, 09 Dec 2021 03:09:17: 17000000 INFO @ Thu, 09 Dec 2021 03:09:19: 12000000 INFO @ Thu, 09 Dec 2021 03:09:23: 24000000 INFO @ Thu, 09 Dec 2021 03:09:23: 18000000 INFO @ Thu, 09 Dec 2021 03:09:25: 13000000 INFO @ Thu, 09 Dec 2021 03:09:28: 25000000 INFO @ Thu, 09 Dec 2021 03:09:29: 19000000 INFO @ Thu, 09 Dec 2021 03:09:31: 14000000 INFO @ Thu, 09 Dec 2021 03:09:34: 26000000 INFO @ Thu, 09 Dec 2021 03:09:34: 20000000 INFO @ Thu, 09 Dec 2021 03:09:37: 15000000 INFO @ Thu, 09 Dec 2021 03:09:40: 27000000 INFO @ Thu, 09 Dec 2021 03:09:40: 21000000 INFO @ Thu, 09 Dec 2021 03:09:43: 16000000 INFO @ Thu, 09 Dec 2021 03:09:46: 28000000 INFO @ Thu, 09 Dec 2021 03:09:46: 22000000 INFO @ Thu, 09 Dec 2021 03:09:49: 17000000 INFO @ Thu, 09 Dec 2021 03:09:52: 29000000 INFO @ Thu, 09 Dec 2021 03:09:52: 23000000 INFO @ Thu, 09 Dec 2021 03:09:54: 18000000 INFO @ Thu, 09 Dec 2021 03:09:57: 30000000 INFO @ Thu, 09 Dec 2021 03:09:58: 24000000 INFO @ Thu, 09 Dec 2021 03:10:00: 19000000 INFO @ Thu, 09 Dec 2021 03:10:03: 31000000 INFO @ Thu, 09 Dec 2021 03:10:03: 25000000 INFO @ Thu, 09 Dec 2021 03:10:06: 20000000 INFO @ Thu, 09 Dec 2021 03:10:09: 32000000 INFO @ Thu, 09 Dec 2021 03:10:09: 26000000 INFO @ Thu, 09 Dec 2021 03:10:12: 21000000 INFO @ Thu, 09 Dec 2021 03:10:15: 33000000 INFO @ Thu, 09 Dec 2021 03:10:15: 27000000 INFO @ Thu, 09 Dec 2021 03:10:18: 22000000 INFO @ Thu, 09 Dec 2021 03:10:21: 34000000 INFO @ Thu, 09 Dec 2021 03:10:21: 28000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 03:10:24: 23000000 INFO @ Thu, 09 Dec 2021 03:10:26: 35000000 INFO @ Thu, 09 Dec 2021 03:10:27: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 03:10:27: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 03:10:27: #1 total tags in treatment: 16322453 INFO @ Thu, 09 Dec 2021 03:10:27: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:10:27: #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 03:10:27: 29000000 INFO @ Thu, 09 Dec 2021 03:10:27: #1 tags after filtering in treatment: 14824248 INFO @ Thu, 09 Dec 2021 03:10:27: #1 Redundant rate of treatment: 0.09 INFO @ Thu, 09 Dec 2021 03:10:27: #1 finished! INFO @ Thu, 09 Dec 2021 03:10:27: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:10:27: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:10:28: #2 number of paired peaks: 324 WARNING @ Thu, 09 Dec 2021 03:10:28: Fewer paired peaks (324) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 324 pairs to build model! INFO @ Thu, 09 Dec 2021 03:10:28: start model_add_line... INFO @ Thu, 09 Dec 2021 03:10:28: start X-correlation... INFO @ Thu, 09 Dec 2021 03:10:28: end of X-cor INFO @ Thu, 09 Dec 2021 03:10:28: #2 finished! INFO @ Thu, 09 Dec 2021 03:10:28: #2 predicted fragment length is 124 bps INFO @ Thu, 09 Dec 2021 03:10:28: #2 alternative fragment length(s) may be 4,124 bps INFO @ Thu, 09 Dec 2021 03:10:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9555458/SRX9555458.05_model.r INFO @ Thu, 09 Dec 2021 03:10:28: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:10:28: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:10:29: 24000000 INFO @ Thu, 09 Dec 2021 03:10:33: 30000000 INFO @ Thu, 09 Dec 2021 03:10:35: 25000000 INFO @ Thu, 09 Dec 2021 03:10:38: 31000000 INFO @ Thu, 09 Dec 2021 03:10:41: 26000000 INFO @ Thu, 09 Dec 2021 03:10:44: 32000000 INFO @ Thu, 09 Dec 2021 03:10:47: 27000000 INFO @ Thu, 09 Dec 2021 03:10:50: 33000000 INFO @ Thu, 09 Dec 2021 03:10:53: 28000000 INFO @ Thu, 09 Dec 2021 03:10:55: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:10:56: 34000000 INFO @ Thu, 09 Dec 2021 03:10:58: 29000000 INFO @ Thu, 09 Dec 2021 03:11:01: 35000000 INFO @ Thu, 09 Dec 2021 03:11:02: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 03:11:02: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 03:11:02: #1 total tags in treatment: 16322453 INFO @ Thu, 09 Dec 2021 03:11:02: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:11:02: #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 03:11:02: #1 tags after filtering in treatment: 14824248 INFO @ Thu, 09 Dec 2021 03:11:02: #1 Redundant rate of treatment: 0.09 INFO @ Thu, 09 Dec 2021 03:11:02: #1 finished! INFO @ Thu, 09 Dec 2021 03:11:02: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:11:02: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:11:03: #2 number of paired peaks: 324 WARNING @ Thu, 09 Dec 2021 03:11:03: Fewer paired peaks (324) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 324 pairs to build model! INFO @ Thu, 09 Dec 2021 03:11:03: start model_add_line... INFO @ Thu, 09 Dec 2021 03:11:03: start X-correlation... INFO @ Thu, 09 Dec 2021 03:11:03: end of X-cor INFO @ Thu, 09 Dec 2021 03:11:03: #2 finished! INFO @ Thu, 09 Dec 2021 03:11:03: #2 predicted fragment length is 124 bps INFO @ Thu, 09 Dec 2021 03:11:03: #2 alternative fragment length(s) may be 4,124 bps INFO @ Thu, 09 Dec 2021 03:11:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9555458/SRX9555458.10_model.r INFO @ Thu, 09 Dec 2021 03:11:03: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:11:03: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:11:04: 30000000 INFO @ Thu, 09 Dec 2021 03:11:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9555458/SRX9555458.05_peaks.xls INFO @ Thu, 09 Dec 2021 03:11:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9555458/SRX9555458.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:11:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9555458/SRX9555458.05_summits.bed INFO @ Thu, 09 Dec 2021 03:11:07: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2412 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:11:09: 31000000 INFO @ Thu, 09 Dec 2021 03:11:14: 32000000 INFO @ Thu, 09 Dec 2021 03:11:20: 33000000 BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 03:11:25: 34000000 INFO @ Thu, 09 Dec 2021 03:11:30: 35000000 INFO @ Thu, 09 Dec 2021 03:11:30: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 03:11:30: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 03:11:30: #1 total tags in treatment: 16322453 INFO @ Thu, 09 Dec 2021 03:11:30: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:11:30: #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 03:11:30: #1 tags after filtering in treatment: 14824248 INFO @ Thu, 09 Dec 2021 03:11:30: #1 Redundant rate of treatment: 0.09 INFO @ Thu, 09 Dec 2021 03:11:30: #1 finished! INFO @ Thu, 09 Dec 2021 03:11:30: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:11:30: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:11:31: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:11:31: #2 number of paired peaks: 324 WARNING @ Thu, 09 Dec 2021 03:11:31: Fewer paired peaks (324) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 324 pairs to build model! INFO @ Thu, 09 Dec 2021 03:11:31: start model_add_line... INFO @ Thu, 09 Dec 2021 03:11:31: start X-correlation... INFO @ Thu, 09 Dec 2021 03:11:31: end of X-cor INFO @ Thu, 09 Dec 2021 03:11:31: #2 finished! INFO @ Thu, 09 Dec 2021 03:11:31: #2 predicted fragment length is 124 bps INFO @ Thu, 09 Dec 2021 03:11:31: #2 alternative fragment length(s) may be 4,124 bps INFO @ Thu, 09 Dec 2021 03:11:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9555458/SRX9555458.20_model.r INFO @ Thu, 09 Dec 2021 03:11:31: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:11:31: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:11:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9555458/SRX9555458.10_peaks.xls INFO @ Thu, 09 Dec 2021 03:11:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9555458/SRX9555458.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:11:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9555458/SRX9555458.10_summits.bed INFO @ Thu, 09 Dec 2021 03:11:44: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1296 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:11:58: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:12:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9555458/SRX9555458.20_peaks.xls INFO @ Thu, 09 Dec 2021 03:12:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9555458/SRX9555458.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:12:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9555458/SRX9555458.20_summits.bed INFO @ Thu, 09 Dec 2021 03:12:10: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (483 records, 4 fields): 2 millis CompletedMACS2peakCalling