Job ID = 14158779 SRX = SRX10342579 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: 00:14:05 19203880 reads; of these: 19203880 (100.00%) were paired; of these: 7039836 (36.66%) aligned concordantly 0 times 10194785 (53.09%) aligned concordantly exactly 1 time 1969259 (10.25%) aligned concordantly >1 times ---- 7039836 pairs aligned concordantly 0 times; of these: 4552652 (64.67%) aligned discordantly 1 time ---- 2487184 pairs aligned 0 times concordantly or discordantly; of these: 4974368 mates make up the pairs; of these: 3103481 (62.39%) aligned 0 times 737124 (14.82%) aligned exactly 1 time 1133763 (22.79%) aligned >1 times 91.92% overall alignment rate Time searching: 00:14:05 Overall time: 00:14:05 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] 4618985 / 16708420 = 0.2764 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 18:11:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10342579/SRX10342579.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10342579/SRX10342579.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10342579/SRX10342579.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10342579/SRX10342579.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 18:11:08: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:11:08: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:11:12: 1000000 INFO @ Wed, 08 Dec 2021 18:11:16: 2000000 INFO @ Wed, 08 Dec 2021 18:11:20: 3000000 INFO @ Wed, 08 Dec 2021 18:11:23: 4000000 INFO @ Wed, 08 Dec 2021 18:11:27: 5000000 INFO @ Wed, 08 Dec 2021 18:11:31: 6000000 INFO @ Wed, 08 Dec 2021 18:11:35: 7000000 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 18:11:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10342579/SRX10342579.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10342579/SRX10342579.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10342579/SRX10342579.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10342579/SRX10342579.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 18:11:38: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:11:38: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:11:38: 8000000 INFO @ Wed, 08 Dec 2021 18:11:42: 1000000 INFO @ Wed, 08 Dec 2021 18:11:42: 9000000 INFO @ Wed, 08 Dec 2021 18:11:46: 2000000 INFO @ Wed, 08 Dec 2021 18:11:46: 10000000 INFO @ Wed, 08 Dec 2021 18:11:50: 3000000 INFO @ Wed, 08 Dec 2021 18:11:50: 11000000 INFO @ Wed, 08 Dec 2021 18:11:54: 4000000 INFO @ Wed, 08 Dec 2021 18:11:54: 12000000 INFO @ Wed, 08 Dec 2021 18:11:57: 5000000 INFO @ Wed, 08 Dec 2021 18:11:58: 13000000 INFO @ Wed, 08 Dec 2021 18:12:01: 6000000 INFO @ Wed, 08 Dec 2021 18:12:02: 14000000 INFO @ Wed, 08 Dec 2021 18:12:05: 7000000 INFO @ Wed, 08 Dec 2021 18:12:06: 15000000 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 18:12:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10342579/SRX10342579.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10342579/SRX10342579.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10342579/SRX10342579.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10342579/SRX10342579.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 18:12:08: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:12:08: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:12:09: 8000000 INFO @ Wed, 08 Dec 2021 18:12:10: 16000000 INFO @ Wed, 08 Dec 2021 18:12:12: 1000000 INFO @ Wed, 08 Dec 2021 18:12:13: 9000000 INFO @ Wed, 08 Dec 2021 18:12:14: 17000000 INFO @ Wed, 08 Dec 2021 18:12:17: 2000000 INFO @ Wed, 08 Dec 2021 18:12:17: 10000000 INFO @ Wed, 08 Dec 2021 18:12:18: 18000000 INFO @ Wed, 08 Dec 2021 18:12:21: 3000000 INFO @ Wed, 08 Dec 2021 18:12:21: 11000000 INFO @ Wed, 08 Dec 2021 18:12:22: 19000000 INFO @ Wed, 08 Dec 2021 18:12:25: 12000000 INFO @ Wed, 08 Dec 2021 18:12:25: 4000000 INFO @ Wed, 08 Dec 2021 18:12:26: 20000000 INFO @ Wed, 08 Dec 2021 18:12:29: 13000000 INFO @ Wed, 08 Dec 2021 18:12:30: 21000000 INFO @ Wed, 08 Dec 2021 18:12:30: 5000000 INFO @ Wed, 08 Dec 2021 18:12:33: 14000000 INFO @ Wed, 08 Dec 2021 18:12:34: 22000000 INFO @ Wed, 08 Dec 2021 18:12:34: 6000000 INFO @ Wed, 08 Dec 2021 18:12:37: 15000000 INFO @ Wed, 08 Dec 2021 18:12:38: 23000000 INFO @ Wed, 08 Dec 2021 18:12:39: 7000000 INFO @ Wed, 08 Dec 2021 18:12:41: 16000000 INFO @ Wed, 08 Dec 2021 18:12:42: 24000000 INFO @ Wed, 08 Dec 2021 18:12:43: 8000000 INFO @ Wed, 08 Dec 2021 18:12:45: 17000000 INFO @ Wed, 08 Dec 2021 18:12:46: 25000000 INFO @ Wed, 08 Dec 2021 18:12:48: 9000000 INFO @ Wed, 08 Dec 2021 18:12:49: 18000000 INFO @ Wed, 08 Dec 2021 18:12:50: 26000000 INFO @ Wed, 08 Dec 2021 18:12:50: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 18:12:50: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 18:12:50: #1 total tags in treatment: 8584476 INFO @ Wed, 08 Dec 2021 18:12:50: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:12:50: #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 18:12:50: #1 tags after filtering in treatment: 7843394 INFO @ Wed, 08 Dec 2021 18:12:50: #1 Redundant rate of treatment: 0.09 INFO @ Wed, 08 Dec 2021 18:12:50: #1 finished! INFO @ Wed, 08 Dec 2021 18:12:50: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:12:50: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:12:51: #2 number of paired peaks: 664 WARNING @ Wed, 08 Dec 2021 18:12:51: Fewer paired peaks (664) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 664 pairs to build model! INFO @ Wed, 08 Dec 2021 18:12:51: start model_add_line... INFO @ Wed, 08 Dec 2021 18:12:51: start X-correlation... INFO @ Wed, 08 Dec 2021 18:12:51: end of X-cor INFO @ Wed, 08 Dec 2021 18:12:51: #2 finished! INFO @ Wed, 08 Dec 2021 18:12:51: #2 predicted fragment length is 144 bps INFO @ Wed, 08 Dec 2021 18:12:51: #2 alternative fragment length(s) may be 4,144 bps INFO @ Wed, 08 Dec 2021 18:12:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10342579/SRX10342579.05_model.r INFO @ Wed, 08 Dec 2021 18:12:51: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:12:51: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:12:52: 10000000 INFO @ Wed, 08 Dec 2021 18:12:53: 19000000 INFO @ Wed, 08 Dec 2021 18:12:57: 20000000 INFO @ Wed, 08 Dec 2021 18:12:57: 11000000 INFO @ Wed, 08 Dec 2021 18:13:01: 21000000 INFO @ Wed, 08 Dec 2021 18:13:01: 12000000 INFO @ Wed, 08 Dec 2021 18:13:05: 22000000 INFO @ Wed, 08 Dec 2021 18:13:06: 13000000 INFO @ Wed, 08 Dec 2021 18:13:06: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:13:08: 23000000 INFO @ Wed, 08 Dec 2021 18:13:10: 14000000 INFO @ Wed, 08 Dec 2021 18:13:12: 24000000 INFO @ Wed, 08 Dec 2021 18:13:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10342579/SRX10342579.05_peaks.xls INFO @ Wed, 08 Dec 2021 18:13:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10342579/SRX10342579.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:13:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10342579/SRX10342579.05_summits.bed INFO @ Wed, 08 Dec 2021 18:13:14: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (450 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:13:15: 15000000 INFO @ Wed, 08 Dec 2021 18:13:16: 25000000 INFO @ Wed, 08 Dec 2021 18:13:19: 16000000 INFO @ Wed, 08 Dec 2021 18:13:20: 26000000 INFO @ Wed, 08 Dec 2021 18:13:20: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 18:13:20: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 18:13:20: #1 total tags in treatment: 8584476 INFO @ Wed, 08 Dec 2021 18:13:20: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:13:20: #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 18:13:20: #1 tags after filtering in treatment: 7843394 INFO @ Wed, 08 Dec 2021 18:13:20: #1 Redundant rate of treatment: 0.09 INFO @ Wed, 08 Dec 2021 18:13:20: #1 finished! INFO @ Wed, 08 Dec 2021 18:13:20: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:13:20: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:13:21: #2 number of paired peaks: 664 WARNING @ Wed, 08 Dec 2021 18:13:21: Fewer paired peaks (664) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 664 pairs to build model! INFO @ Wed, 08 Dec 2021 18:13:21: start model_add_line... INFO @ Wed, 08 Dec 2021 18:13:21: start X-correlation... INFO @ Wed, 08 Dec 2021 18:13:21: end of X-cor INFO @ Wed, 08 Dec 2021 18:13:21: #2 finished! INFO @ Wed, 08 Dec 2021 18:13:21: #2 predicted fragment length is 144 bps INFO @ Wed, 08 Dec 2021 18:13:21: #2 alternative fragment length(s) may be 4,144 bps INFO @ Wed, 08 Dec 2021 18:13:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10342579/SRX10342579.10_model.r INFO @ Wed, 08 Dec 2021 18:13:21: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:13:21: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:13:23: 17000000 INFO @ Wed, 08 Dec 2021 18:13:28: 18000000 INFO @ Wed, 08 Dec 2021 18:13:32: 19000000 INFO @ Wed, 08 Dec 2021 18:13:37: 20000000 INFO @ Wed, 08 Dec 2021 18:13:37: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:13:41: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 18:13:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10342579/SRX10342579.10_peaks.xls INFO @ Wed, 08 Dec 2021 18:13:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10342579/SRX10342579.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:13:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10342579/SRX10342579.10_summits.bed INFO @ Wed, 08 Dec 2021 18:13:45: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (344 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:13:45: 22000000 INFO @ Wed, 08 Dec 2021 18:13:49: 23000000 INFO @ Wed, 08 Dec 2021 18:13:54: 24000000 INFO @ Wed, 08 Dec 2021 18:13:58: 25000000 INFO @ Wed, 08 Dec 2021 18:14:02: 26000000 INFO @ Wed, 08 Dec 2021 18:14:03: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 18:14:03: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 18:14:03: #1 total tags in treatment: 8584476 INFO @ Wed, 08 Dec 2021 18:14:03: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:14:03: #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 18:14:03: #1 tags after filtering in treatment: 7843394 INFO @ Wed, 08 Dec 2021 18:14:03: #1 Redundant rate of treatment: 0.09 INFO @ Wed, 08 Dec 2021 18:14:03: #1 finished! INFO @ Wed, 08 Dec 2021 18:14:03: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:14:03: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:14:03: #2 number of paired peaks: 664 WARNING @ Wed, 08 Dec 2021 18:14:03: Fewer paired peaks (664) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 664 pairs to build model! INFO @ Wed, 08 Dec 2021 18:14:03: start model_add_line... INFO @ Wed, 08 Dec 2021 18:14:03: start X-correlation... INFO @ Wed, 08 Dec 2021 18:14:03: end of X-cor INFO @ Wed, 08 Dec 2021 18:14:03: #2 finished! INFO @ Wed, 08 Dec 2021 18:14:03: #2 predicted fragment length is 144 bps INFO @ Wed, 08 Dec 2021 18:14:03: #2 alternative fragment length(s) may be 4,144 bps INFO @ Wed, 08 Dec 2021 18:14:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10342579/SRX10342579.20_model.r INFO @ Wed, 08 Dec 2021 18:14:04: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:14:04: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:14:20: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:14:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10342579/SRX10342579.20_peaks.xls INFO @ Wed, 08 Dec 2021 18:14:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10342579/SRX10342579.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:14:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10342579/SRX10342579.20_summits.bed INFO @ Wed, 08 Dec 2021 18:14:27: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (228 records, 4 fields): 11 millis CompletedMACS2peakCalling BigWig に変換しました。