Job ID = 14158909 SRX = SRX10342596 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:15:13 22931718 reads; of these: 22931718 (100.00%) were paired; of these: 2623001 (11.44%) aligned concordantly 0 times 17963938 (78.34%) aligned concordantly exactly 1 time 2344779 (10.23%) aligned concordantly >1 times ---- 2623001 pairs aligned concordantly 0 times; of these: 1661512 (63.34%) aligned discordantly 1 time ---- 961489 pairs aligned 0 times concordantly or discordantly; of these: 1922978 mates make up the pairs; of these: 1212134 (63.03%) aligned 0 times 307586 (16.00%) aligned exactly 1 time 403258 (20.97%) aligned >1 times 97.36% overall alignment rate Time searching: 00:15:14 Overall time: 00:15:14 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] 1779993 / 21946980 = 0.0811 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 18:42:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10342596/SRX10342596.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10342596/SRX10342596.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10342596/SRX10342596.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10342596/SRX10342596.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 18:42:15: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:42:15: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:42:19: 1000000 INFO @ Wed, 08 Dec 2021 18:42:24: 2000000 INFO @ Wed, 08 Dec 2021 18:42:28: 3000000 INFO @ Wed, 08 Dec 2021 18:42:32: 4000000 INFO @ Wed, 08 Dec 2021 18:42:37: 5000000 INFO @ Wed, 08 Dec 2021 18:42:41: 6000000 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 18:42:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10342596/SRX10342596.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10342596/SRX10342596.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10342596/SRX10342596.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10342596/SRX10342596.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 18:42:45: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:42:45: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:42:45: 7000000 INFO @ Wed, 08 Dec 2021 18:42:49: 1000000 INFO @ Wed, 08 Dec 2021 18:42:50: 8000000 INFO @ Wed, 08 Dec 2021 18:42:53: 2000000 INFO @ Wed, 08 Dec 2021 18:42:54: 9000000 INFO @ Wed, 08 Dec 2021 18:42:57: 3000000 INFO @ Wed, 08 Dec 2021 18:42:59: 10000000 INFO @ Wed, 08 Dec 2021 18:43:00: 4000000 INFO @ Wed, 08 Dec 2021 18:43:03: 11000000 INFO @ Wed, 08 Dec 2021 18:43:04: 5000000 INFO @ Wed, 08 Dec 2021 18:43:08: 12000000 INFO @ Wed, 08 Dec 2021 18:43:08: 6000000 INFO @ Wed, 08 Dec 2021 18:43:12: 7000000 INFO @ Wed, 08 Dec 2021 18:43:12: 13000000 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 18:43:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10342596/SRX10342596.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10342596/SRX10342596.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10342596/SRX10342596.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10342596/SRX10342596.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 18:43:15: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:43:15: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:43:16: 8000000 INFO @ Wed, 08 Dec 2021 18:43:17: 14000000 INFO @ Wed, 08 Dec 2021 18:43:19: 1000000 INFO @ Wed, 08 Dec 2021 18:43:20: 9000000 INFO @ Wed, 08 Dec 2021 18:43:21: 15000000 INFO @ Wed, 08 Dec 2021 18:43:23: 2000000 INFO @ Wed, 08 Dec 2021 18:43:24: 10000000 INFO @ Wed, 08 Dec 2021 18:43:25: 16000000 INFO @ Wed, 08 Dec 2021 18:43:26: 3000000 INFO @ Wed, 08 Dec 2021 18:43:27: 11000000 INFO @ Wed, 08 Dec 2021 18:43:30: 17000000 INFO @ Wed, 08 Dec 2021 18:43:30: 4000000 INFO @ Wed, 08 Dec 2021 18:43:31: 12000000 INFO @ Wed, 08 Dec 2021 18:43:34: 18000000 INFO @ Wed, 08 Dec 2021 18:43:34: 5000000 INFO @ Wed, 08 Dec 2021 18:43:35: 13000000 INFO @ Wed, 08 Dec 2021 18:43:38: 6000000 INFO @ Wed, 08 Dec 2021 18:43:39: 19000000 INFO @ Wed, 08 Dec 2021 18:43:39: 14000000 INFO @ Wed, 08 Dec 2021 18:43:42: 7000000 INFO @ Wed, 08 Dec 2021 18:43:43: 20000000 INFO @ Wed, 08 Dec 2021 18:43:43: 15000000 INFO @ Wed, 08 Dec 2021 18:43:46: 8000000 INFO @ Wed, 08 Dec 2021 18:43:47: 16000000 INFO @ Wed, 08 Dec 2021 18:43:47: 21000000 INFO @ Wed, 08 Dec 2021 18:43:50: 9000000 INFO @ Wed, 08 Dec 2021 18:43:51: 17000000 INFO @ Wed, 08 Dec 2021 18:43:52: 22000000 INFO @ Wed, 08 Dec 2021 18:43:54: 10000000 INFO @ Wed, 08 Dec 2021 18:43:55: 18000000 INFO @ Wed, 08 Dec 2021 18:43:56: 23000000 INFO @ Wed, 08 Dec 2021 18:43:58: 11000000 INFO @ Wed, 08 Dec 2021 18:43:59: 19000000 INFO @ Wed, 08 Dec 2021 18:44:01: 24000000 INFO @ Wed, 08 Dec 2021 18:44:01: 12000000 INFO @ Wed, 08 Dec 2021 18:44:02: 20000000 INFO @ Wed, 08 Dec 2021 18:44:05: 25000000 INFO @ Wed, 08 Dec 2021 18:44:05: 13000000 INFO @ Wed, 08 Dec 2021 18:44:06: 21000000 INFO @ Wed, 08 Dec 2021 18:44:09: 14000000 INFO @ Wed, 08 Dec 2021 18:44:09: 26000000 INFO @ Wed, 08 Dec 2021 18:44:10: 22000000 INFO @ Wed, 08 Dec 2021 18:44:13: 15000000 INFO @ Wed, 08 Dec 2021 18:44:14: 27000000 INFO @ Wed, 08 Dec 2021 18:44:14: 23000000 INFO @ Wed, 08 Dec 2021 18:44:17: 16000000 INFO @ Wed, 08 Dec 2021 18:44:18: 24000000 INFO @ Wed, 08 Dec 2021 18:44:18: 28000000 INFO @ Wed, 08 Dec 2021 18:44:21: 17000000 INFO @ Wed, 08 Dec 2021 18:44:22: 25000000 INFO @ Wed, 08 Dec 2021 18:44:23: 29000000 INFO @ Wed, 08 Dec 2021 18:44:25: 18000000 INFO @ Wed, 08 Dec 2021 18:44:26: 26000000 INFO @ Wed, 08 Dec 2021 18:44:27: 30000000 INFO @ Wed, 08 Dec 2021 18:44:29: 19000000 INFO @ Wed, 08 Dec 2021 18:44:30: 27000000 INFO @ Wed, 08 Dec 2021 18:44:31: 31000000 INFO @ Wed, 08 Dec 2021 18:44:33: 20000000 INFO @ Wed, 08 Dec 2021 18:44:34: 28000000 INFO @ Wed, 08 Dec 2021 18:44:36: 32000000 INFO @ Wed, 08 Dec 2021 18:44:36: 21000000 INFO @ Wed, 08 Dec 2021 18:44:37: 29000000 INFO @ Wed, 08 Dec 2021 18:44:40: 22000000 INFO @ Wed, 08 Dec 2021 18:44:40: 33000000 INFO @ Wed, 08 Dec 2021 18:44:41: 30000000 INFO @ Wed, 08 Dec 2021 18:44:44: 23000000 INFO @ Wed, 08 Dec 2021 18:44:45: 34000000 INFO @ Wed, 08 Dec 2021 18:44:45: 31000000 INFO @ Wed, 08 Dec 2021 18:44:48: 24000000 INFO @ Wed, 08 Dec 2021 18:44:49: 32000000 INFO @ Wed, 08 Dec 2021 18:44:49: 35000000 INFO @ Wed, 08 Dec 2021 18:44:52: 25000000 INFO @ Wed, 08 Dec 2021 18:44:53: 33000000 INFO @ Wed, 08 Dec 2021 18:44:54: 36000000 INFO @ Wed, 08 Dec 2021 18:44:56: 26000000 INFO @ Wed, 08 Dec 2021 18:44:57: 34000000 INFO @ Wed, 08 Dec 2021 18:44:58: 37000000 INFO @ Wed, 08 Dec 2021 18:45:00: 27000000 INFO @ Wed, 08 Dec 2021 18:45:01: 35000000 INFO @ Wed, 08 Dec 2021 18:45:02: 38000000 INFO @ Wed, 08 Dec 2021 18:45:04: 28000000 INFO @ Wed, 08 Dec 2021 18:45:04: 36000000 INFO @ Wed, 08 Dec 2021 18:45:07: 39000000 INFO @ Wed, 08 Dec 2021 18:45:08: 29000000 INFO @ Wed, 08 Dec 2021 18:45:08: 37000000 INFO @ Wed, 08 Dec 2021 18:45:11: 40000000 INFO @ Wed, 08 Dec 2021 18:45:11: 30000000 INFO @ Wed, 08 Dec 2021 18:45:12: 38000000 INFO @ Wed, 08 Dec 2021 18:45:15: 31000000 INFO @ Wed, 08 Dec 2021 18:45:16: 41000000 INFO @ Wed, 08 Dec 2021 18:45:16: 39000000 INFO @ Wed, 08 Dec 2021 18:45:16: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 18:45:16: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 18:45:16: #1 total tags in treatment: 18628647 INFO @ Wed, 08 Dec 2021 18:45:16: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:45:16: #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 18:45:17: #1 tags after filtering in treatment: 16958549 INFO @ Wed, 08 Dec 2021 18:45:17: #1 Redundant rate of treatment: 0.09 INFO @ Wed, 08 Dec 2021 18:45:17: #1 finished! INFO @ Wed, 08 Dec 2021 18:45:17: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:45:17: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:45:18: #2 number of paired peaks: 239 WARNING @ Wed, 08 Dec 2021 18:45:18: Fewer paired peaks (239) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 239 pairs to build model! INFO @ Wed, 08 Dec 2021 18:45:18: start model_add_line... INFO @ Wed, 08 Dec 2021 18:45:18: start X-correlation... INFO @ Wed, 08 Dec 2021 18:45:18: end of X-cor INFO @ Wed, 08 Dec 2021 18:45:18: #2 finished! INFO @ Wed, 08 Dec 2021 18:45:18: #2 predicted fragment length is 96 bps INFO @ Wed, 08 Dec 2021 18:45:18: #2 alternative fragment length(s) may be 3,75,96 bps INFO @ Wed, 08 Dec 2021 18:45:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10342596/SRX10342596.05_model.r INFO @ Wed, 08 Dec 2021 18:45:18: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:45:18: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:45:19: 32000000 INFO @ Wed, 08 Dec 2021 18:45:20: 40000000 INFO @ Wed, 08 Dec 2021 18:45:23: 33000000 INFO @ Wed, 08 Dec 2021 18:45:24: 41000000 INFO @ Wed, 08 Dec 2021 18:45:24: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 18:45:24: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 18:45:24: #1 total tags in treatment: 18628647 INFO @ Wed, 08 Dec 2021 18:45:24: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:45:24: #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 18:45:25: #1 tags after filtering in treatment: 16958549 INFO @ Wed, 08 Dec 2021 18:45:25: #1 Redundant rate of treatment: 0.09 INFO @ Wed, 08 Dec 2021 18:45:25: #1 finished! INFO @ Wed, 08 Dec 2021 18:45:25: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:45:25: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:45:26: #2 number of paired peaks: 239 WARNING @ Wed, 08 Dec 2021 18:45:26: Fewer paired peaks (239) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 239 pairs to build model! INFO @ Wed, 08 Dec 2021 18:45:26: start model_add_line... INFO @ Wed, 08 Dec 2021 18:45:26: start X-correlation... INFO @ Wed, 08 Dec 2021 18:45:26: end of X-cor INFO @ Wed, 08 Dec 2021 18:45:26: #2 finished! INFO @ Wed, 08 Dec 2021 18:45:26: #2 predicted fragment length is 96 bps INFO @ Wed, 08 Dec 2021 18:45:26: #2 alternative fragment length(s) may be 3,75,96 bps INFO @ Wed, 08 Dec 2021 18:45:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10342596/SRX10342596.10_model.r INFO @ Wed, 08 Dec 2021 18:45:26: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:45:26: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:45:27: 34000000 INFO @ Wed, 08 Dec 2021 18:45:31: 35000000 INFO @ Wed, 08 Dec 2021 18:45:34: 36000000 INFO @ Wed, 08 Dec 2021 18:45:38: 37000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 18:45:42: 38000000 INFO @ Wed, 08 Dec 2021 18:45:46: 39000000 INFO @ Wed, 08 Dec 2021 18:45:46: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:45:50: 40000000 INFO @ Wed, 08 Dec 2021 18:45:53: 41000000 INFO @ Wed, 08 Dec 2021 18:45:54: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 18:45:54: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 18:45:54: #1 total tags in treatment: 18628647 INFO @ Wed, 08 Dec 2021 18:45:54: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:45:54: #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 18:45:54: #1 tags after filtering in treatment: 16958549 INFO @ Wed, 08 Dec 2021 18:45:54: #1 Redundant rate of treatment: 0.09 INFO @ Wed, 08 Dec 2021 18:45:54: #1 finished! INFO @ Wed, 08 Dec 2021 18:45:54: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:45:54: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:45:55: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:45:55: #2 number of paired peaks: 239 WARNING @ Wed, 08 Dec 2021 18:45:55: Fewer paired peaks (239) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 239 pairs to build model! INFO @ Wed, 08 Dec 2021 18:45:55: start model_add_line... INFO @ Wed, 08 Dec 2021 18:45:55: start X-correlation... INFO @ Wed, 08 Dec 2021 18:45:55: end of X-cor INFO @ Wed, 08 Dec 2021 18:45:55: #2 finished! INFO @ Wed, 08 Dec 2021 18:45:55: #2 predicted fragment length is 96 bps INFO @ Wed, 08 Dec 2021 18:45:55: #2 alternative fragment length(s) may be 3,75,96 bps INFO @ Wed, 08 Dec 2021 18:45:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10342596/SRX10342596.20_model.r INFO @ Wed, 08 Dec 2021 18:45:55: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:45:55: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:46:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10342596/SRX10342596.05_peaks.xls INFO @ Wed, 08 Dec 2021 18:46:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10342596/SRX10342596.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:46:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10342596/SRX10342596.05_summits.bed INFO @ Wed, 08 Dec 2021 18:46:00: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2600 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:46:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10342596/SRX10342596.10_peaks.xls INFO @ Wed, 08 Dec 2021 18:46:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10342596/SRX10342596.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:46:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10342596/SRX10342596.10_summits.bed INFO @ Wed, 08 Dec 2021 18:46:09: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (590 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:46:25: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:46:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10342596/SRX10342596.20_peaks.xls INFO @ Wed, 08 Dec 2021 18:46:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10342596/SRX10342596.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:46:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10342596/SRX10342596.20_summits.bed INFO @ Wed, 08 Dec 2021 18:46:40: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (177 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。