Job ID = 14158930 SRX = SRX10342597 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: 00:13:32 20823464 reads; of these: 20823464 (100.00%) were paired; of these: 3536133 (16.98%) aligned concordantly 0 times 15324617 (73.59%) aligned concordantly exactly 1 time 1962714 (9.43%) aligned concordantly >1 times ---- 3536133 pairs aligned concordantly 0 times; of these: 2416878 (68.35%) aligned discordantly 1 time ---- 1119255 pairs aligned 0 times concordantly or discordantly; of these: 2238510 mates make up the pairs; of these: 1268759 (56.68%) aligned 0 times 405208 (18.10%) aligned exactly 1 time 564543 (25.22%) aligned >1 times 96.95% overall alignment rate Time searching: 00:13:32 Overall time: 00:13:32 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] 2880124 / 19690509 = 0.1463 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 18:48:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10342597/SRX10342597.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10342597/SRX10342597.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10342597/SRX10342597.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10342597/SRX10342597.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 18:48:03: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:48:03: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:48:08: 1000000 INFO @ Wed, 08 Dec 2021 18:48:12: 2000000 INFO @ Wed, 08 Dec 2021 18:48:16: 3000000 INFO @ Wed, 08 Dec 2021 18:48:20: 4000000 INFO @ Wed, 08 Dec 2021 18:48:24: 5000000 INFO @ Wed, 08 Dec 2021 18:48:28: 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 18:48:33: 7000000 INFO @ Wed, 08 Dec 2021 18:48:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10342597/SRX10342597.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10342597/SRX10342597.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10342597/SRX10342597.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10342597/SRX10342597.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 18:48:33: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:48:33: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:48:37: 8000000 INFO @ Wed, 08 Dec 2021 18:48:38: 1000000 INFO @ Wed, 08 Dec 2021 18:48:42: 9000000 INFO @ Wed, 08 Dec 2021 18:48:42: 2000000 INFO @ Wed, 08 Dec 2021 18:48:46: 10000000 INFO @ Wed, 08 Dec 2021 18:48:47: 3000000 INFO @ Wed, 08 Dec 2021 18:48:51: 11000000 INFO @ Wed, 08 Dec 2021 18:48:51: 4000000 INFO @ Wed, 08 Dec 2021 18:48:55: 12000000 INFO @ Wed, 08 Dec 2021 18:48:56: 5000000 INFO @ Wed, 08 Dec 2021 18:49:00: 13000000 INFO @ Wed, 08 Dec 2021 18:49:00: 6000000 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 18:49:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10342597/SRX10342597.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10342597/SRX10342597.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10342597/SRX10342597.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10342597/SRX10342597.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 18:49:03: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:49:03: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:49:04: 14000000 INFO @ Wed, 08 Dec 2021 18:49:05: 7000000 INFO @ Wed, 08 Dec 2021 18:49:09: 1000000 INFO @ Wed, 08 Dec 2021 18:49:09: 15000000 INFO @ Wed, 08 Dec 2021 18:49:10: 8000000 INFO @ Wed, 08 Dec 2021 18:49:14: 16000000 INFO @ Wed, 08 Dec 2021 18:49:14: 2000000 INFO @ Wed, 08 Dec 2021 18:49:14: 9000000 INFO @ Wed, 08 Dec 2021 18:49:19: 17000000 INFO @ Wed, 08 Dec 2021 18:49:19: 10000000 INFO @ Wed, 08 Dec 2021 18:49:20: 3000000 INFO @ Wed, 08 Dec 2021 18:49:24: 18000000 INFO @ Wed, 08 Dec 2021 18:49:24: 11000000 INFO @ Wed, 08 Dec 2021 18:49:25: 4000000 INFO @ Wed, 08 Dec 2021 18:49:28: 19000000 INFO @ Wed, 08 Dec 2021 18:49:29: 12000000 INFO @ Wed, 08 Dec 2021 18:49:31: 5000000 INFO @ Wed, 08 Dec 2021 18:49:33: 20000000 INFO @ Wed, 08 Dec 2021 18:49:34: 13000000 INFO @ Wed, 08 Dec 2021 18:49:37: 6000000 INFO @ Wed, 08 Dec 2021 18:49:38: 21000000 INFO @ Wed, 08 Dec 2021 18:49:38: 14000000 INFO @ Wed, 08 Dec 2021 18:49:42: 7000000 INFO @ Wed, 08 Dec 2021 18:49:43: 22000000 INFO @ Wed, 08 Dec 2021 18:49:43: 15000000 INFO @ Wed, 08 Dec 2021 18:49:48: 23000000 INFO @ Wed, 08 Dec 2021 18:49:48: 8000000 INFO @ Wed, 08 Dec 2021 18:49:48: 16000000 INFO @ Wed, 08 Dec 2021 18:49:52: 24000000 INFO @ Wed, 08 Dec 2021 18:49:53: 17000000 INFO @ Wed, 08 Dec 2021 18:49:53: 9000000 INFO @ Wed, 08 Dec 2021 18:49:57: 25000000 INFO @ Wed, 08 Dec 2021 18:49:58: 18000000 INFO @ Wed, 08 Dec 2021 18:49:59: 10000000 INFO @ Wed, 08 Dec 2021 18:50:02: 26000000 INFO @ Wed, 08 Dec 2021 18:50:02: 19000000 INFO @ Wed, 08 Dec 2021 18:50:05: 11000000 INFO @ Wed, 08 Dec 2021 18:50:07: 27000000 INFO @ Wed, 08 Dec 2021 18:50:07: 20000000 INFO @ Wed, 08 Dec 2021 18:50:10: 12000000 INFO @ Wed, 08 Dec 2021 18:50:12: 28000000 INFO @ Wed, 08 Dec 2021 18:50:12: 21000000 INFO @ Wed, 08 Dec 2021 18:50:16: 13000000 INFO @ Wed, 08 Dec 2021 18:50:16: 29000000 INFO @ Wed, 08 Dec 2021 18:50:17: 22000000 INFO @ Wed, 08 Dec 2021 18:50:21: 30000000 INFO @ Wed, 08 Dec 2021 18:50:21: 14000000 INFO @ Wed, 08 Dec 2021 18:50:22: 23000000 INFO @ Wed, 08 Dec 2021 18:50:26: 31000000 INFO @ Wed, 08 Dec 2021 18:50:27: 24000000 INFO @ Wed, 08 Dec 2021 18:50:27: 15000000 INFO @ Wed, 08 Dec 2021 18:50:31: 32000000 INFO @ Wed, 08 Dec 2021 18:50:31: 25000000 INFO @ Wed, 08 Dec 2021 18:50:32: 16000000 INFO @ Wed, 08 Dec 2021 18:50:35: 33000000 INFO @ Wed, 08 Dec 2021 18:50:36: 26000000 INFO @ Wed, 08 Dec 2021 18:50:38: 17000000 INFO @ Wed, 08 Dec 2021 18:50:40: 34000000 INFO @ Wed, 08 Dec 2021 18:50:41: 27000000 INFO @ Wed, 08 Dec 2021 18:50:43: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 18:50:43: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 18:50:43: #1 total tags in treatment: 14684196 INFO @ Wed, 08 Dec 2021 18:50:43: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:50:43: #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 18:50:43: #1 tags after filtering in treatment: 13504175 INFO @ Wed, 08 Dec 2021 18:50:43: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 18:50:43: #1 finished! INFO @ Wed, 08 Dec 2021 18:50:43: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:50:43: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:50:44: 18000000 INFO @ Wed, 08 Dec 2021 18:50:44: #2 number of paired peaks: 320 WARNING @ Wed, 08 Dec 2021 18:50:44: Fewer paired peaks (320) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 320 pairs to build model! INFO @ Wed, 08 Dec 2021 18:50:44: start model_add_line... INFO @ Wed, 08 Dec 2021 18:50:44: start X-correlation... INFO @ Wed, 08 Dec 2021 18:50:44: end of X-cor INFO @ Wed, 08 Dec 2021 18:50:44: #2 finished! INFO @ Wed, 08 Dec 2021 18:50:44: #2 predicted fragment length is 167 bps INFO @ Wed, 08 Dec 2021 18:50:44: #2 alternative fragment length(s) may be 4,131,167 bps INFO @ Wed, 08 Dec 2021 18:50:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10342597/SRX10342597.05_model.r INFO @ Wed, 08 Dec 2021 18:50:44: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:50:44: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:50:46: 28000000 INFO @ Wed, 08 Dec 2021 18:50:49: 19000000 INFO @ Wed, 08 Dec 2021 18:50:50: 29000000 INFO @ Wed, 08 Dec 2021 18:50:55: 20000000 INFO @ Wed, 08 Dec 2021 18:50:55: 30000000 INFO @ Wed, 08 Dec 2021 18:51:00: 31000000 INFO @ Wed, 08 Dec 2021 18:51:00: 21000000 INFO @ Wed, 08 Dec 2021 18:51:05: 32000000 INFO @ Wed, 08 Dec 2021 18:51:06: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 18:51:09: 33000000 INFO @ Wed, 08 Dec 2021 18:51:10: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:51:11: 23000000 INFO @ Wed, 08 Dec 2021 18:51:14: 34000000 INFO @ Wed, 08 Dec 2021 18:51:17: 24000000 INFO @ Wed, 08 Dec 2021 18:51:17: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 18:51:17: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 18:51:17: #1 total tags in treatment: 14684196 INFO @ Wed, 08 Dec 2021 18:51:17: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:51:17: #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 18:51:17: #1 tags after filtering in treatment: 13504175 INFO @ Wed, 08 Dec 2021 18:51:17: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 18:51:17: #1 finished! INFO @ Wed, 08 Dec 2021 18:51:17: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:51:17: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:51:18: #2 number of paired peaks: 320 WARNING @ Wed, 08 Dec 2021 18:51:18: Fewer paired peaks (320) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 320 pairs to build model! INFO @ Wed, 08 Dec 2021 18:51:18: start model_add_line... INFO @ Wed, 08 Dec 2021 18:51:18: start X-correlation... INFO @ Wed, 08 Dec 2021 18:51:18: end of X-cor INFO @ Wed, 08 Dec 2021 18:51:18: #2 finished! INFO @ Wed, 08 Dec 2021 18:51:18: #2 predicted fragment length is 167 bps INFO @ Wed, 08 Dec 2021 18:51:18: #2 alternative fragment length(s) may be 4,131,167 bps INFO @ Wed, 08 Dec 2021 18:51:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10342597/SRX10342597.10_model.r INFO @ Wed, 08 Dec 2021 18:51:18: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:51:18: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:51:22: 25000000 INFO @ Wed, 08 Dec 2021 18:51:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10342597/SRX10342597.05_peaks.xls INFO @ Wed, 08 Dec 2021 18:51:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10342597/SRX10342597.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:51:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10342597/SRX10342597.05_summits.bed INFO @ Wed, 08 Dec 2021 18:51:23: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4454 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:51:27: 26000000 INFO @ Wed, 08 Dec 2021 18:51:33: 27000000 INFO @ Wed, 08 Dec 2021 18:51:38: 28000000 INFO @ Wed, 08 Dec 2021 18:51:43: 29000000 INFO @ Wed, 08 Dec 2021 18:51:45: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:51:48: 30000000 INFO @ Wed, 08 Dec 2021 18:51:53: 31000000 INFO @ Wed, 08 Dec 2021 18:51:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10342597/SRX10342597.10_peaks.xls INFO @ Wed, 08 Dec 2021 18:51:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10342597/SRX10342597.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:51:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10342597/SRX10342597.10_summits.bed INFO @ Wed, 08 Dec 2021 18:51:58: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (2098 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:51:58: 32000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 18:52:03: 33000000 INFO @ Wed, 08 Dec 2021 18:52:09: 34000000 INFO @ Wed, 08 Dec 2021 18:52:12: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 18:52:12: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 18:52:12: #1 total tags in treatment: 14684196 INFO @ Wed, 08 Dec 2021 18:52:12: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:52:12: #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 18:52:12: #1 tags after filtering in treatment: 13504175 INFO @ Wed, 08 Dec 2021 18:52:12: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 18:52:12: #1 finished! INFO @ Wed, 08 Dec 2021 18:52:12: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:52:12: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:52:13: #2 number of paired peaks: 320 WARNING @ Wed, 08 Dec 2021 18:52:13: Fewer paired peaks (320) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 320 pairs to build model! INFO @ Wed, 08 Dec 2021 18:52:13: start model_add_line... INFO @ Wed, 08 Dec 2021 18:52:13: start X-correlation... INFO @ Wed, 08 Dec 2021 18:52:13: end of X-cor INFO @ Wed, 08 Dec 2021 18:52:13: #2 finished! INFO @ Wed, 08 Dec 2021 18:52:13: #2 predicted fragment length is 167 bps INFO @ Wed, 08 Dec 2021 18:52:13: #2 alternative fragment length(s) may be 4,131,167 bps INFO @ Wed, 08 Dec 2021 18:52:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10342597/SRX10342597.20_model.r INFO @ Wed, 08 Dec 2021 18:52:13: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:52:13: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:52:38: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:52:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10342597/SRX10342597.20_peaks.xls INFO @ Wed, 08 Dec 2021 18:52:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10342597/SRX10342597.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:52:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10342597/SRX10342597.20_summits.bed INFO @ Wed, 08 Dec 2021 18:52:50: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (482 records, 4 fields): 2 millis CompletedMACS2peakCalling