Job ID = 14159399 SRX = SRX8976742 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: 00:11:51 14852355 reads; of these: 14852355 (100.00%) were paired; of these: 1212148 (8.16%) aligned concordantly 0 times 11701317 (78.78%) aligned concordantly exactly 1 time 1938890 (13.05%) aligned concordantly >1 times ---- 1212148 pairs aligned concordantly 0 times; of these: 841509 (69.42%) aligned discordantly 1 time ---- 370639 pairs aligned 0 times concordantly or discordantly; of these: 741278 mates make up the pairs; of these: 246849 (33.30%) aligned 0 times 230229 (31.06%) aligned exactly 1 time 264200 (35.64%) aligned >1 times 99.17% overall alignment rate Time searching: 00:11:51 Overall time: 00:11:51 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] 435071 / 14448460 = 0.0301 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 21:49:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976742/SRX8976742.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976742/SRX8976742.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976742/SRX8976742.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976742/SRX8976742.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 21:49:45: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:49:45: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:49:50: 1000000 INFO @ Wed, 08 Dec 2021 21:49:55: 2000000 INFO @ Wed, 08 Dec 2021 21:50:01: 3000000 INFO @ Wed, 08 Dec 2021 21:50:05: 4000000 INFO @ Wed, 08 Dec 2021 21:50:10: 5000000 INFO @ Wed, 08 Dec 2021 21:50:15: 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 21:50:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976742/SRX8976742.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976742/SRX8976742.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976742/SRX8976742.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976742/SRX8976742.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 21:50:19: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:50:19: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:50:20: 7000000 INFO @ Wed, 08 Dec 2021 21:50:25: 1000000 INFO @ Wed, 08 Dec 2021 21:50:26: 8000000 INFO @ Wed, 08 Dec 2021 21:50:31: 2000000 INFO @ Wed, 08 Dec 2021 21:50:32: 9000000 INFO @ Wed, 08 Dec 2021 21:50:37: 3000000 INFO @ Wed, 08 Dec 2021 21:50:38: 10000000 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 21:50:43: 4000000 INFO @ Wed, 08 Dec 2021 21:50:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976742/SRX8976742.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976742/SRX8976742.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976742/SRX8976742.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976742/SRX8976742.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 21:50:44: #1 read tag files... INFO @ Wed, 08 Dec 2021 21:50:44: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 21:50:44: 11000000 INFO @ Wed, 08 Dec 2021 21:50:49: 5000000 INFO @ Wed, 08 Dec 2021 21:50:50: 12000000 INFO @ Wed, 08 Dec 2021 21:50:50: 1000000 INFO @ Wed, 08 Dec 2021 21:50:55: 6000000 INFO @ Wed, 08 Dec 2021 21:50:56: 2000000 INFO @ Wed, 08 Dec 2021 21:50:56: 13000000 INFO @ Wed, 08 Dec 2021 21:51:01: 7000000 INFO @ Wed, 08 Dec 2021 21:51:02: 3000000 INFO @ Wed, 08 Dec 2021 21:51:02: 14000000 INFO @ Wed, 08 Dec 2021 21:51:07: 8000000 INFO @ Wed, 08 Dec 2021 21:51:08: 15000000 INFO @ Wed, 08 Dec 2021 21:51:08: 4000000 INFO @ Wed, 08 Dec 2021 21:51:13: 9000000 INFO @ Wed, 08 Dec 2021 21:51:14: 5000000 INFO @ Wed, 08 Dec 2021 21:51:14: 16000000 INFO @ Wed, 08 Dec 2021 21:51:19: 10000000 INFO @ Wed, 08 Dec 2021 21:51:20: 6000000 INFO @ Wed, 08 Dec 2021 21:51:20: 17000000 INFO @ Wed, 08 Dec 2021 21:51:25: 11000000 INFO @ Wed, 08 Dec 2021 21:51:26: 7000000 INFO @ Wed, 08 Dec 2021 21:51:26: 18000000 INFO @ Wed, 08 Dec 2021 21:51:31: 12000000 INFO @ Wed, 08 Dec 2021 21:51:31: 8000000 INFO @ Wed, 08 Dec 2021 21:51:32: 19000000 INFO @ Wed, 08 Dec 2021 21:51:36: 13000000 INFO @ Wed, 08 Dec 2021 21:51:37: 9000000 INFO @ Wed, 08 Dec 2021 21:51:37: 20000000 INFO @ Wed, 08 Dec 2021 21:51:42: 14000000 INFO @ Wed, 08 Dec 2021 21:51:43: 10000000 INFO @ Wed, 08 Dec 2021 21:51:43: 21000000 INFO @ Wed, 08 Dec 2021 21:51:48: 15000000 INFO @ Wed, 08 Dec 2021 21:51:49: 11000000 INFO @ Wed, 08 Dec 2021 21:51:49: 22000000 INFO @ Wed, 08 Dec 2021 21:51:54: 16000000 INFO @ Wed, 08 Dec 2021 21:51:54: 12000000 INFO @ Wed, 08 Dec 2021 21:51:55: 23000000 INFO @ Wed, 08 Dec 2021 21:52:00: 17000000 INFO @ Wed, 08 Dec 2021 21:52:00: 13000000 INFO @ Wed, 08 Dec 2021 21:52:01: 24000000 INFO @ Wed, 08 Dec 2021 21:52:05: 18000000 INFO @ Wed, 08 Dec 2021 21:52:06: 14000000 INFO @ Wed, 08 Dec 2021 21:52:07: 25000000 INFO @ Wed, 08 Dec 2021 21:52:11: 19000000 INFO @ Wed, 08 Dec 2021 21:52:12: 15000000 INFO @ Wed, 08 Dec 2021 21:52:12: 26000000 INFO @ Wed, 08 Dec 2021 21:52:17: 20000000 INFO @ Wed, 08 Dec 2021 21:52:18: 16000000 INFO @ Wed, 08 Dec 2021 21:52:18: 27000000 INFO @ Wed, 08 Dec 2021 21:52:22: 21000000 INFO @ Wed, 08 Dec 2021 21:52:23: 17000000 INFO @ Wed, 08 Dec 2021 21:52:24: 28000000 INFO @ Wed, 08 Dec 2021 21:52:27: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 21:52:27: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 21:52:27: #1 total tags in treatment: 13223736 INFO @ Wed, 08 Dec 2021 21:52:27: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:52:27: #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 21:52:28: #1 tags after filtering in treatment: 12249957 INFO @ Wed, 08 Dec 2021 21:52:28: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 21:52:28: #1 finished! INFO @ Wed, 08 Dec 2021 21:52:28: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:52:28: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:52:28: 22000000 INFO @ Wed, 08 Dec 2021 21:52:28: #2 number of paired peaks: 334 WARNING @ Wed, 08 Dec 2021 21:52:28: Fewer paired peaks (334) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 334 pairs to build model! INFO @ Wed, 08 Dec 2021 21:52:28: start model_add_line... INFO @ Wed, 08 Dec 2021 21:52:29: start X-correlation... INFO @ Wed, 08 Dec 2021 21:52:29: end of X-cor INFO @ Wed, 08 Dec 2021 21:52:29: #2 finished! INFO @ Wed, 08 Dec 2021 21:52:29: #2 predicted fragment length is 157 bps INFO @ Wed, 08 Dec 2021 21:52:29: #2 alternative fragment length(s) may be 4,157 bps INFO @ Wed, 08 Dec 2021 21:52:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976742/SRX8976742.05_model.r INFO @ Wed, 08 Dec 2021 21:52:29: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:52:29: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 21:52:29: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 21:52:34: 23000000 INFO @ Wed, 08 Dec 2021 21:52:35: 19000000 INFO @ Wed, 08 Dec 2021 21:52:40: 24000000 INFO @ Wed, 08 Dec 2021 21:52:40: 20000000 INFO @ Wed, 08 Dec 2021 21:52:46: 25000000 INFO @ Wed, 08 Dec 2021 21:52:46: 21000000 INFO @ Wed, 08 Dec 2021 21:52:51: 26000000 INFO @ Wed, 08 Dec 2021 21:52:52: 22000000 INFO @ Wed, 08 Dec 2021 21:52:53: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:52:57: 27000000 INFO @ Wed, 08 Dec 2021 21:52:57: 23000000 INFO @ Wed, 08 Dec 2021 21:53:03: 28000000 INFO @ Wed, 08 Dec 2021 21:53:03: 24000000 INFO @ Wed, 08 Dec 2021 21:53:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976742/SRX8976742.05_peaks.xls INFO @ Wed, 08 Dec 2021 21:53:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976742/SRX8976742.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:53:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976742/SRX8976742.05_summits.bed INFO @ Wed, 08 Dec 2021 21:53:04: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (349 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 21:53:06: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 21:53:06: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 21:53:06: #1 total tags in treatment: 13223736 INFO @ Wed, 08 Dec 2021 21:53:06: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:53:06: #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 21:53:06: #1 tags after filtering in treatment: 12249957 INFO @ Wed, 08 Dec 2021 21:53:06: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 21:53:06: #1 finished! INFO @ Wed, 08 Dec 2021 21:53:06: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:53:06: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:53:07: #2 number of paired peaks: 334 WARNING @ Wed, 08 Dec 2021 21:53:07: Fewer paired peaks (334) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 334 pairs to build model! INFO @ Wed, 08 Dec 2021 21:53:07: start model_add_line... INFO @ Wed, 08 Dec 2021 21:53:07: start X-correlation... INFO @ Wed, 08 Dec 2021 21:53:07: end of X-cor INFO @ Wed, 08 Dec 2021 21:53:07: #2 finished! INFO @ Wed, 08 Dec 2021 21:53:07: #2 predicted fragment length is 157 bps INFO @ Wed, 08 Dec 2021 21:53:07: #2 alternative fragment length(s) may be 4,157 bps INFO @ Wed, 08 Dec 2021 21:53:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976742/SRX8976742.10_model.r INFO @ Wed, 08 Dec 2021 21:53:07: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:53:07: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 21:53:09: 25000000 INFO @ Wed, 08 Dec 2021 21:53:14: 26000000 INFO @ Wed, 08 Dec 2021 21:53:18: 27000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 21:53:23: 28000000 INFO @ Wed, 08 Dec 2021 21:53:26: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 21:53:26: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 21:53:26: #1 total tags in treatment: 13223736 INFO @ Wed, 08 Dec 2021 21:53:26: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 21:53:26: #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 21:53:26: #1 tags after filtering in treatment: 12249957 INFO @ Wed, 08 Dec 2021 21:53:26: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 21:53:26: #1 finished! INFO @ Wed, 08 Dec 2021 21:53:26: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 21:53:26: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 21:53:27: #2 number of paired peaks: 334 WARNING @ Wed, 08 Dec 2021 21:53:27: Fewer paired peaks (334) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 334 pairs to build model! INFO @ Wed, 08 Dec 2021 21:53:27: start model_add_line... INFO @ Wed, 08 Dec 2021 21:53:27: start X-correlation... INFO @ Wed, 08 Dec 2021 21:53:27: end of X-cor INFO @ Wed, 08 Dec 2021 21:53:27: #2 finished! INFO @ Wed, 08 Dec 2021 21:53:27: #2 predicted fragment length is 157 bps INFO @ Wed, 08 Dec 2021 21:53:27: #2 alternative fragment length(s) may be 4,157 bps INFO @ Wed, 08 Dec 2021 21:53:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976742/SRX8976742.20_model.r INFO @ Wed, 08 Dec 2021 21:53:27: #3 Call peaks... INFO @ Wed, 08 Dec 2021 21:53:27: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 21:53:31: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:53:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976742/SRX8976742.10_peaks.xls INFO @ Wed, 08 Dec 2021 21:53:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976742/SRX8976742.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:53:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976742/SRX8976742.10_summits.bed INFO @ Wed, 08 Dec 2021 21:53:42: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (262 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 21:53:52: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 21:54:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976742/SRX8976742.20_peaks.xls INFO @ Wed, 08 Dec 2021 21:54:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976742/SRX8976742.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 21:54:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976742/SRX8976742.20_summits.bed INFO @ Wed, 08 Dec 2021 21:54:03: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (187 records, 4 fields): 1 millis CompletedMACS2peakCalling