Job ID = 14159243 SRX = SRX8976712 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: 00:14:54 13582578 reads; of these: 13582578 (100.00%) were paired; of these: 284648 (2.10%) aligned concordantly 0 times 11526062 (84.86%) aligned concordantly exactly 1 time 1771868 (13.05%) aligned concordantly >1 times ---- 284648 pairs aligned concordantly 0 times; of these: 83875 (29.47%) aligned discordantly 1 time ---- 200773 pairs aligned 0 times concordantly or discordantly; of these: 401546 mates make up the pairs; of these: 246856 (61.48%) aligned 0 times 110034 (27.40%) aligned exactly 1 time 44656 (11.12%) aligned >1 times 99.09% overall alignment rate Time searching: 00:14:54 Overall time: 00:14:54 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] 187466 / 13366582 = 0.0140 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 20:52:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976712/SRX8976712.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976712/SRX8976712.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976712/SRX8976712.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976712/SRX8976712.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 20:52:13: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:52:13: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:52:23: 1000000 INFO @ Wed, 08 Dec 2021 20:52:33: 2000000 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 20:52:42: 3000000 INFO @ Wed, 08 Dec 2021 20:52:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976712/SRX8976712.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976712/SRX8976712.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976712/SRX8976712.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976712/SRX8976712.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 20:52:43: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:52:43: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:52:52: 1000000 INFO @ Wed, 08 Dec 2021 20:52:52: 4000000 INFO @ Wed, 08 Dec 2021 20:53:00: 2000000 INFO @ Wed, 08 Dec 2021 20:53:03: 5000000 INFO @ Wed, 08 Dec 2021 20:53:09: 3000000 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 20:53:13: 6000000 INFO @ Wed, 08 Dec 2021 20:53:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976712/SRX8976712.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976712/SRX8976712.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976712/SRX8976712.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976712/SRX8976712.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 20:53:13: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:53:13: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:53:17: 4000000 INFO @ Wed, 08 Dec 2021 20:53:23: 7000000 INFO @ Wed, 08 Dec 2021 20:53:24: 1000000 INFO @ Wed, 08 Dec 2021 20:53:26: 5000000 INFO @ Wed, 08 Dec 2021 20:53:33: 8000000 INFO @ Wed, 08 Dec 2021 20:53:34: 2000000 INFO @ Wed, 08 Dec 2021 20:53:34: 6000000 INFO @ Wed, 08 Dec 2021 20:53:43: 7000000 INFO @ Wed, 08 Dec 2021 20:53:43: 9000000 INFO @ Wed, 08 Dec 2021 20:53:45: 3000000 INFO @ Wed, 08 Dec 2021 20:53:52: 8000000 INFO @ Wed, 08 Dec 2021 20:53:54: 10000000 INFO @ Wed, 08 Dec 2021 20:53:55: 4000000 INFO @ Wed, 08 Dec 2021 20:54:00: 9000000 INFO @ Wed, 08 Dec 2021 20:54:04: 11000000 INFO @ Wed, 08 Dec 2021 20:54:06: 5000000 INFO @ Wed, 08 Dec 2021 20:54:09: 10000000 INFO @ Wed, 08 Dec 2021 20:54:15: 12000000 INFO @ Wed, 08 Dec 2021 20:54:17: 6000000 INFO @ Wed, 08 Dec 2021 20:54:18: 11000000 INFO @ Wed, 08 Dec 2021 20:54:26: 13000000 INFO @ Wed, 08 Dec 2021 20:54:26: 12000000 INFO @ Wed, 08 Dec 2021 20:54:27: 7000000 INFO @ Wed, 08 Dec 2021 20:54:35: 13000000 INFO @ Wed, 08 Dec 2021 20:54:36: 14000000 INFO @ Wed, 08 Dec 2021 20:54:38: 8000000 INFO @ Wed, 08 Dec 2021 20:54:44: 14000000 INFO @ Wed, 08 Dec 2021 20:54:46: 15000000 INFO @ Wed, 08 Dec 2021 20:54:48: 9000000 INFO @ Wed, 08 Dec 2021 20:54:52: 15000000 INFO @ Wed, 08 Dec 2021 20:54:57: 16000000 INFO @ Wed, 08 Dec 2021 20:54:59: 10000000 INFO @ Wed, 08 Dec 2021 20:55:01: 16000000 INFO @ Wed, 08 Dec 2021 20:55:07: 17000000 INFO @ Wed, 08 Dec 2021 20:55:09: 11000000 INFO @ Wed, 08 Dec 2021 20:55:10: 17000000 INFO @ Wed, 08 Dec 2021 20:55:17: 18000000 INFO @ Wed, 08 Dec 2021 20:55:19: 18000000 INFO @ Wed, 08 Dec 2021 20:55:20: 12000000 INFO @ Wed, 08 Dec 2021 20:55:28: 19000000 INFO @ Wed, 08 Dec 2021 20:55:28: 19000000 INFO @ Wed, 08 Dec 2021 20:55:30: 13000000 INFO @ Wed, 08 Dec 2021 20:55:37: 20000000 INFO @ Wed, 08 Dec 2021 20:55:38: 20000000 INFO @ Wed, 08 Dec 2021 20:55:41: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 20:55:46: 21000000 INFO @ Wed, 08 Dec 2021 20:55:49: 21000000 INFO @ Wed, 08 Dec 2021 20:55:51: 15000000 INFO @ Wed, 08 Dec 2021 20:55:55: 22000000 INFO @ Wed, 08 Dec 2021 20:55:59: 22000000 INFO @ Wed, 08 Dec 2021 20:56:02: 16000000 INFO @ Wed, 08 Dec 2021 20:56:04: 23000000 INFO @ Wed, 08 Dec 2021 20:56:09: 23000000 INFO @ Wed, 08 Dec 2021 20:56:13: 17000000 INFO @ Wed, 08 Dec 2021 20:56:13: 24000000 INFO @ Wed, 08 Dec 2021 20:56:20: 24000000 INFO @ Wed, 08 Dec 2021 20:56:22: 25000000 INFO @ Wed, 08 Dec 2021 20:56:23: 18000000 INFO @ Wed, 08 Dec 2021 20:56:30: 25000000 INFO @ Wed, 08 Dec 2021 20:56:31: 26000000 INFO @ Wed, 08 Dec 2021 20:56:34: 19000000 INFO @ Wed, 08 Dec 2021 20:56:36: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 20:56:36: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 20:56:36: #1 total tags in treatment: 13111112 INFO @ Wed, 08 Dec 2021 20:56:36: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:56:36: #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 20:56:37: #1 tags after filtering in treatment: 12273467 INFO @ Wed, 08 Dec 2021 20:56:37: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 08 Dec 2021 20:56:37: #1 finished! INFO @ Wed, 08 Dec 2021 20:56:37: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:56:37: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:56:38: #2 number of paired peaks: 316 WARNING @ Wed, 08 Dec 2021 20:56:38: Fewer paired peaks (316) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 316 pairs to build model! INFO @ Wed, 08 Dec 2021 20:56:38: start model_add_line... INFO @ Wed, 08 Dec 2021 20:56:38: start X-correlation... INFO @ Wed, 08 Dec 2021 20:56:38: end of X-cor INFO @ Wed, 08 Dec 2021 20:56:38: #2 finished! INFO @ Wed, 08 Dec 2021 20:56:38: #2 predicted fragment length is 149 bps INFO @ Wed, 08 Dec 2021 20:56:38: #2 alternative fragment length(s) may be 4,149 bps INFO @ Wed, 08 Dec 2021 20:56:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976712/SRX8976712.10_model.r INFO @ Wed, 08 Dec 2021 20:56:38: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:56:38: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:56:41: 26000000 INFO @ Wed, 08 Dec 2021 20:56:44: 20000000 INFO @ Wed, 08 Dec 2021 20:56:46: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 20:56:46: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 20:56:46: #1 total tags in treatment: 13111112 INFO @ Wed, 08 Dec 2021 20:56:46: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:56:46: #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 20:56:46: #1 tags after filtering in treatment: 12273467 INFO @ Wed, 08 Dec 2021 20:56:46: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 08 Dec 2021 20:56:46: #1 finished! INFO @ Wed, 08 Dec 2021 20:56:46: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:56:46: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:56:47: #2 number of paired peaks: 316 WARNING @ Wed, 08 Dec 2021 20:56:47: Fewer paired peaks (316) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 316 pairs to build model! INFO @ Wed, 08 Dec 2021 20:56:47: start model_add_line... INFO @ Wed, 08 Dec 2021 20:56:47: start X-correlation... INFO @ Wed, 08 Dec 2021 20:56:47: end of X-cor INFO @ Wed, 08 Dec 2021 20:56:47: #2 finished! INFO @ Wed, 08 Dec 2021 20:56:47: #2 predicted fragment length is 149 bps INFO @ Wed, 08 Dec 2021 20:56:47: #2 alternative fragment length(s) may be 4,149 bps INFO @ Wed, 08 Dec 2021 20:56:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976712/SRX8976712.05_model.r INFO @ Wed, 08 Dec 2021 20:56:47: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:56:47: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:56:54: 21000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 20:57:03: 22000000 INFO @ Wed, 08 Dec 2021 20:57:11: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 20:57:13: 23000000 INFO @ Wed, 08 Dec 2021 20:57:20: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 20:57:23: 24000000 INFO @ Wed, 08 Dec 2021 20:57:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976712/SRX8976712.10_peaks.xls INFO @ Wed, 08 Dec 2021 20:57:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976712/SRX8976712.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:57:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976712/SRX8976712.10_summits.bed INFO @ Wed, 08 Dec 2021 20:57:25: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (280 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 20:57:32: 25000000 INFO @ Wed, 08 Dec 2021 20:57:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976712/SRX8976712.05_peaks.xls INFO @ Wed, 08 Dec 2021 20:57:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976712/SRX8976712.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:57:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976712/SRX8976712.05_summits.bed INFO @ Wed, 08 Dec 2021 20:57:35: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (365 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 20:57:42: 26000000 INFO @ Wed, 08 Dec 2021 20:57:47: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 20:57:47: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 20:57:47: #1 total tags in treatment: 13111112 INFO @ Wed, 08 Dec 2021 20:57:47: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:57:47: #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 20:57:48: #1 tags after filtering in treatment: 12273467 INFO @ Wed, 08 Dec 2021 20:57:48: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 08 Dec 2021 20:57:48: #1 finished! INFO @ Wed, 08 Dec 2021 20:57:48: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:57:48: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:57:49: #2 number of paired peaks: 316 WARNING @ Wed, 08 Dec 2021 20:57:49: Fewer paired peaks (316) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 316 pairs to build model! INFO @ Wed, 08 Dec 2021 20:57:49: start model_add_line... INFO @ Wed, 08 Dec 2021 20:57:49: start X-correlation... INFO @ Wed, 08 Dec 2021 20:57:49: end of X-cor INFO @ Wed, 08 Dec 2021 20:57:49: #2 finished! INFO @ Wed, 08 Dec 2021 20:57:49: #2 predicted fragment length is 149 bps INFO @ Wed, 08 Dec 2021 20:57:49: #2 alternative fragment length(s) may be 4,149 bps INFO @ Wed, 08 Dec 2021 20:57:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976712/SRX8976712.20_model.r INFO @ Wed, 08 Dec 2021 20:57:49: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:57:49: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:58:22: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 20:58:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976712/SRX8976712.20_peaks.xls INFO @ Wed, 08 Dec 2021 20:58:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976712/SRX8976712.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:58:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976712/SRX8976712.20_summits.bed INFO @ Wed, 08 Dec 2021 20:58:36: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (184 records, 4 fields): 2 millis CompletedMACS2peakCalling