Job ID = 12265425 SRX = SRX7246268 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: 00:26:45 34161503 reads; of these: 34161503 (100.00%) were paired; of these: 2784117 (8.15%) aligned concordantly 0 times 28091140 (82.23%) aligned concordantly exactly 1 time 3286246 (9.62%) aligned concordantly >1 times ---- 2784117 pairs aligned concordantly 0 times; of these: 1219000 (43.78%) aligned discordantly 1 time ---- 1565117 pairs aligned 0 times concordantly or discordantly; of these: 3130234 mates make up the pairs; of these: 2440325 (77.96%) aligned 0 times 381035 (12.17%) aligned exactly 1 time 308874 (9.87%) aligned >1 times 96.43% overall alignment rate Time searching: 00:26:45 Overall time: 00:26:45 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 28 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] 12400763 / 32498113 = 0.3816 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:39:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7246268/SRX7246268.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7246268/SRX7246268.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7246268/SRX7246268.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7246268/SRX7246268.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 @ Sat, 03 Apr 2021 07:39:42: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:39:42: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:39:47: 1000000 INFO @ Sat, 03 Apr 2021 07:39:52: 2000000 INFO @ Sat, 03 Apr 2021 07:39:58: 3000000 INFO @ Sat, 03 Apr 2021 07:40:03: 4000000 INFO @ Sat, 03 Apr 2021 07:40:08: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:40:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7246268/SRX7246268.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7246268/SRX7246268.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7246268/SRX7246268.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7246268/SRX7246268.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 @ Sat, 03 Apr 2021 07:40:12: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:40:12: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:40:13: 6000000 INFO @ Sat, 03 Apr 2021 07:40:18: 1000000 INFO @ Sat, 03 Apr 2021 07:40:18: 7000000 INFO @ Sat, 03 Apr 2021 07:40:23: 2000000 INFO @ Sat, 03 Apr 2021 07:40:24: 8000000 INFO @ Sat, 03 Apr 2021 07:40:28: 3000000 INFO @ Sat, 03 Apr 2021 07:40:29: 9000000 INFO @ Sat, 03 Apr 2021 07:40:34: 4000000 INFO @ Sat, 03 Apr 2021 07:40:35: 10000000 INFO @ Sat, 03 Apr 2021 07:40:39: 5000000 INFO @ Sat, 03 Apr 2021 07:40:40: 11000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:40:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX7246268/SRX7246268.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX7246268/SRX7246268.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX7246268/SRX7246268.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX7246268/SRX7246268.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 @ Sat, 03 Apr 2021 07:40:42: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:40:42: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:40:45: 6000000 INFO @ Sat, 03 Apr 2021 07:40:46: 12000000 INFO @ Sat, 03 Apr 2021 07:40:47: 1000000 INFO @ Sat, 03 Apr 2021 07:40:50: 7000000 INFO @ Sat, 03 Apr 2021 07:40:51: 13000000 INFO @ Sat, 03 Apr 2021 07:40:52: 2000000 INFO @ Sat, 03 Apr 2021 07:40:56: 8000000 INFO @ Sat, 03 Apr 2021 07:40:57: 14000000 INFO @ Sat, 03 Apr 2021 07:40:57: 3000000 INFO @ Sat, 03 Apr 2021 07:41:01: 9000000 INFO @ Sat, 03 Apr 2021 07:41:02: 15000000 INFO @ Sat, 03 Apr 2021 07:41:02: 4000000 INFO @ Sat, 03 Apr 2021 07:41:07: 10000000 INFO @ Sat, 03 Apr 2021 07:41:07: 5000000 INFO @ Sat, 03 Apr 2021 07:41:07: 16000000 INFO @ Sat, 03 Apr 2021 07:41:12: 6000000 INFO @ Sat, 03 Apr 2021 07:41:12: 11000000 INFO @ Sat, 03 Apr 2021 07:41:13: 17000000 INFO @ Sat, 03 Apr 2021 07:41:17: 7000000 INFO @ Sat, 03 Apr 2021 07:41:18: 12000000 INFO @ Sat, 03 Apr 2021 07:41:18: 18000000 INFO @ Sat, 03 Apr 2021 07:41:22: 8000000 INFO @ Sat, 03 Apr 2021 07:41:23: 13000000 INFO @ Sat, 03 Apr 2021 07:41:24: 19000000 INFO @ Sat, 03 Apr 2021 07:41:27: 9000000 INFO @ Sat, 03 Apr 2021 07:41:29: 14000000 INFO @ Sat, 03 Apr 2021 07:41:29: 20000000 INFO @ Sat, 03 Apr 2021 07:41:32: 10000000 INFO @ Sat, 03 Apr 2021 07:41:34: 15000000 INFO @ Sat, 03 Apr 2021 07:41:35: 21000000 INFO @ Sat, 03 Apr 2021 07:41:37: 11000000 INFO @ Sat, 03 Apr 2021 07:41:40: 16000000 INFO @ Sat, 03 Apr 2021 07:41:40: 22000000 INFO @ Sat, 03 Apr 2021 07:41:42: 12000000 INFO @ Sat, 03 Apr 2021 07:41:45: 23000000 INFO @ Sat, 03 Apr 2021 07:41:46: 17000000 INFO @ Sat, 03 Apr 2021 07:41:47: 13000000 INFO @ Sat, 03 Apr 2021 07:41:51: 24000000 INFO @ Sat, 03 Apr 2021 07:41:51: 18000000 INFO @ Sat, 03 Apr 2021 07:41:51: 14000000 INFO @ Sat, 03 Apr 2021 07:41:56: 15000000 INFO @ Sat, 03 Apr 2021 07:41:56: 25000000 INFO @ Sat, 03 Apr 2021 07:41:57: 19000000 INFO @ Sat, 03 Apr 2021 07:42:01: 16000000 INFO @ Sat, 03 Apr 2021 07:42:02: 26000000 INFO @ Sat, 03 Apr 2021 07:42:02: 20000000 INFO @ Sat, 03 Apr 2021 07:42:06: 17000000 INFO @ Sat, 03 Apr 2021 07:42:08: 21000000 INFO @ Sat, 03 Apr 2021 07:42:08: 27000000 INFO @ Sat, 03 Apr 2021 07:42:11: 18000000 INFO @ Sat, 03 Apr 2021 07:42:13: 22000000 INFO @ Sat, 03 Apr 2021 07:42:13: 28000000 INFO @ Sat, 03 Apr 2021 07:42:16: 19000000 INFO @ Sat, 03 Apr 2021 07:42:19: 23000000 INFO @ Sat, 03 Apr 2021 07:42:19: 29000000 INFO @ Sat, 03 Apr 2021 07:42:21: 20000000 INFO @ Sat, 03 Apr 2021 07:42:24: 30000000 INFO @ Sat, 03 Apr 2021 07:42:24: 24000000 INFO @ Sat, 03 Apr 2021 07:42:26: 21000000 INFO @ Sat, 03 Apr 2021 07:42:30: 31000000 INFO @ Sat, 03 Apr 2021 07:42:30: 25000000 INFO @ Sat, 03 Apr 2021 07:42:30: 22000000 INFO @ Sat, 03 Apr 2021 07:42:35: 32000000 INFO @ Sat, 03 Apr 2021 07:42:35: 23000000 INFO @ Sat, 03 Apr 2021 07:42:36: 26000000 INFO @ Sat, 03 Apr 2021 07:42:40: 24000000 INFO @ Sat, 03 Apr 2021 07:42:40: 33000000 INFO @ Sat, 03 Apr 2021 07:42:41: 27000000 INFO @ Sat, 03 Apr 2021 07:42:45: 25000000 INFO @ Sat, 03 Apr 2021 07:42:46: 34000000 INFO @ Sat, 03 Apr 2021 07:42:47: 28000000 INFO @ Sat, 03 Apr 2021 07:42:50: 26000000 INFO @ Sat, 03 Apr 2021 07:42:51: 35000000 INFO @ Sat, 03 Apr 2021 07:42:53: 29000000 INFO @ Sat, 03 Apr 2021 07:42:55: 27000000 INFO @ Sat, 03 Apr 2021 07:42:57: 36000000 INFO @ Sat, 03 Apr 2021 07:42:58: 30000000 INFO @ Sat, 03 Apr 2021 07:43:00: 28000000 INFO @ Sat, 03 Apr 2021 07:43:02: 37000000 INFO @ Sat, 03 Apr 2021 07:43:03: 31000000 INFO @ Sat, 03 Apr 2021 07:43:05: 29000000 INFO @ Sat, 03 Apr 2021 07:43:07: 38000000 INFO @ Sat, 03 Apr 2021 07:43:09: 32000000 INFO @ Sat, 03 Apr 2021 07:43:09: 30000000 INFO @ Sat, 03 Apr 2021 07:43:13: 39000000 INFO @ Sat, 03 Apr 2021 07:43:14: 33000000 INFO @ Sat, 03 Apr 2021 07:43:14: 31000000 INFO @ Sat, 03 Apr 2021 07:43:18: 40000000 INFO @ Sat, 03 Apr 2021 07:43:19: 32000000 INFO @ Sat, 03 Apr 2021 07:43:19: 34000000 INFO @ Sat, 03 Apr 2021 07:43:23: 41000000 INFO @ Sat, 03 Apr 2021 07:43:24: 33000000 INFO @ Sat, 03 Apr 2021 07:43:24: #1 tag size is determined as 51 bps INFO @ Sat, 03 Apr 2021 07:43:24: #1 tag size = 51 INFO @ Sat, 03 Apr 2021 07:43:24: #1 total tags in treatment: 19171396 INFO @ Sat, 03 Apr 2021 07:43:24: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:43:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:43:24: #1 tags after filtering in treatment: 12152690 INFO @ Sat, 03 Apr 2021 07:43:24: #1 Redundant rate of treatment: 0.37 INFO @ Sat, 03 Apr 2021 07:43:24: #1 finished! INFO @ Sat, 03 Apr 2021 07:43:24: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:43:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:43:25: 35000000 INFO @ Sat, 03 Apr 2021 07:43:25: #2 number of paired peaks: 665 WARNING @ Sat, 03 Apr 2021 07:43:25: Fewer paired peaks (665) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 665 pairs to build model! INFO @ Sat, 03 Apr 2021 07:43:25: start model_add_line... INFO @ Sat, 03 Apr 2021 07:43:25: start X-correlation... INFO @ Sat, 03 Apr 2021 07:43:25: end of X-cor INFO @ Sat, 03 Apr 2021 07:43:25: #2 finished! INFO @ Sat, 03 Apr 2021 07:43:25: #2 predicted fragment length is 107 bps INFO @ Sat, 03 Apr 2021 07:43:25: #2 alternative fragment length(s) may be 107 bps INFO @ Sat, 03 Apr 2021 07:43:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7246268/SRX7246268.05_model.r INFO @ Sat, 03 Apr 2021 07:43:25: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:43:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:43:28: 34000000 INFO @ Sat, 03 Apr 2021 07:43:30: 36000000 INFO @ Sat, 03 Apr 2021 07:43:33: 35000000 INFO @ Sat, 03 Apr 2021 07:43:35: 37000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 07:43:38: 36000000 INFO @ Sat, 03 Apr 2021 07:43:41: 38000000 INFO @ Sat, 03 Apr 2021 07:43:43: 37000000 INFO @ Sat, 03 Apr 2021 07:43:46: 39000000 INFO @ Sat, 03 Apr 2021 07:43:47: 38000000 INFO @ Sat, 03 Apr 2021 07:43:51: 40000000 INFO @ Sat, 03 Apr 2021 07:43:52: 39000000 INFO @ Sat, 03 Apr 2021 07:43:55: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:43:56: 41000000 INFO @ Sat, 03 Apr 2021 07:43:57: 40000000 INFO @ Sat, 03 Apr 2021 07:43:57: #1 tag size is determined as 51 bps INFO @ Sat, 03 Apr 2021 07:43:57: #1 tag size = 51 INFO @ Sat, 03 Apr 2021 07:43:57: #1 total tags in treatment: 19171396 INFO @ Sat, 03 Apr 2021 07:43:57: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:43:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:43:57: #1 tags after filtering in treatment: 12152690 INFO @ Sat, 03 Apr 2021 07:43:57: #1 Redundant rate of treatment: 0.37 INFO @ Sat, 03 Apr 2021 07:43:57: #1 finished! INFO @ Sat, 03 Apr 2021 07:43:57: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:43:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:43:58: #2 number of paired peaks: 665 WARNING @ Sat, 03 Apr 2021 07:43:58: Fewer paired peaks (665) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 665 pairs to build model! INFO @ Sat, 03 Apr 2021 07:43:58: start model_add_line... INFO @ Sat, 03 Apr 2021 07:43:58: start X-correlation... INFO @ Sat, 03 Apr 2021 07:43:58: end of X-cor INFO @ Sat, 03 Apr 2021 07:43:58: #2 finished! INFO @ Sat, 03 Apr 2021 07:43:58: #2 predicted fragment length is 107 bps INFO @ Sat, 03 Apr 2021 07:43:58: #2 alternative fragment length(s) may be 107 bps INFO @ Sat, 03 Apr 2021 07:43:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7246268/SRX7246268.10_model.r INFO @ Sat, 03 Apr 2021 07:43:58: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:43:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:44:01: 41000000 INFO @ Sat, 03 Apr 2021 07:44:02: #1 tag size is determined as 51 bps INFO @ Sat, 03 Apr 2021 07:44:02: #1 tag size = 51 INFO @ Sat, 03 Apr 2021 07:44:02: #1 total tags in treatment: 19171396 INFO @ Sat, 03 Apr 2021 07:44:02: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:44:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:44:02: #1 tags after filtering in treatment: 12152690 INFO @ Sat, 03 Apr 2021 07:44:02: #1 Redundant rate of treatment: 0.37 INFO @ Sat, 03 Apr 2021 07:44:02: #1 finished! INFO @ Sat, 03 Apr 2021 07:44:02: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:44:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:44:03: #2 number of paired peaks: 665 WARNING @ Sat, 03 Apr 2021 07:44:03: Fewer paired peaks (665) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 665 pairs to build model! INFO @ Sat, 03 Apr 2021 07:44:03: start model_add_line... INFO @ Sat, 03 Apr 2021 07:44:03: start X-correlation... INFO @ Sat, 03 Apr 2021 07:44:03: end of X-cor INFO @ Sat, 03 Apr 2021 07:44:03: #2 finished! INFO @ Sat, 03 Apr 2021 07:44:03: #2 predicted fragment length is 107 bps INFO @ Sat, 03 Apr 2021 07:44:03: #2 alternative fragment length(s) may be 107 bps INFO @ Sat, 03 Apr 2021 07:44:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX7246268/SRX7246268.20_model.r INFO @ Sat, 03 Apr 2021 07:44:03: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:44:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:44:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7246268/SRX7246268.05_peaks.xls INFO @ Sat, 03 Apr 2021 07:44:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7246268/SRX7246268.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:44:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7246268/SRX7246268.05_summits.bed INFO @ Sat, 03 Apr 2021 07:44:10: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (8139 records, 4 fields): 9 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 07:44:27: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:44:31: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:44:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7246268/SRX7246268.10_peaks.xls INFO @ Sat, 03 Apr 2021 07:44:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7246268/SRX7246268.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:44:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7246268/SRX7246268.10_summits.bed INFO @ Sat, 03 Apr 2021 07:44:42: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (5233 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:44:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX7246268/SRX7246268.20_peaks.xls INFO @ Sat, 03 Apr 2021 07:44:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX7246268/SRX7246268.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:44:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX7246268/SRX7246268.20_summits.bed INFO @ Sat, 03 Apr 2021 07:44:45: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2457 records, 4 fields): 4 millis CompletedMACS2peakCalling