Job ID = 6367666 SRX = SRX3733160 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T23:33:35 prefetch.2.10.7: 1) Downloading 'SRR6760673'... 2020-06-15T23:33:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:42:46 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:42:47 prefetch.2.10.7: 1) 'SRR6760673' was downloaded successfully 2020-06-15T23:42:47 prefetch.2.10.7: 'SRR6760673' has 0 unresolved dependencies Read 27439278 spots for SRR6760673/SRR6760673.sra Written 27439278 spots for SRR6760673/SRR6760673.sra 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: 00:33:12 27439278 reads; of these: 27439278 (100.00%) were paired; of these: 1750725 (6.38%) aligned concordantly 0 times 22940047 (83.60%) aligned concordantly exactly 1 time 2748506 (10.02%) aligned concordantly >1 times ---- 1750725 pairs aligned concordantly 0 times; of these: 346802 (19.81%) aligned discordantly 1 time ---- 1403923 pairs aligned 0 times concordantly or discordantly; of these: 2807846 mates make up the pairs; of these: 2180152 (77.64%) aligned 0 times 409413 (14.58%) aligned exactly 1 time 218281 (7.77%) aligned >1 times 96.03% overall alignment rate Time searching: 00:33:12 Overall time: 00:33:12 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 24 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] 16625642 / 25999804 = 0.6395 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 09:31:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3733160/SRX3733160.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3733160/SRX3733160.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3733160/SRX3733160.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3733160/SRX3733160.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 @ Tue, 16 Jun 2020 09:31:47: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:31:47: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:31:56: 1000000 INFO @ Tue, 16 Jun 2020 09:32:04: 2000000 INFO @ Tue, 16 Jun 2020 09:32:12: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 09:32:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3733160/SRX3733160.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3733160/SRX3733160.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3733160/SRX3733160.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3733160/SRX3733160.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 @ Tue, 16 Jun 2020 09:32:17: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:32:17: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:32:21: 4000000 INFO @ Tue, 16 Jun 2020 09:32:26: 1000000 INFO @ Tue, 16 Jun 2020 09:32:30: 5000000 INFO @ Tue, 16 Jun 2020 09:32:35: 2000000 INFO @ Tue, 16 Jun 2020 09:32:39: 6000000 INFO @ Tue, 16 Jun 2020 09:32:44: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 09:32:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3733160/SRX3733160.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3733160/SRX3733160.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3733160/SRX3733160.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3733160/SRX3733160.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 @ Tue, 16 Jun 2020 09:32:47: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:32:47: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:32:48: 7000000 INFO @ Tue, 16 Jun 2020 09:32:53: 4000000 INFO @ Tue, 16 Jun 2020 09:32:57: 1000000 INFO @ Tue, 16 Jun 2020 09:32:57: 8000000 INFO @ Tue, 16 Jun 2020 09:33:02: 5000000 INFO @ Tue, 16 Jun 2020 09:33:06: 2000000 INFO @ Tue, 16 Jun 2020 09:33:06: 9000000 INFO @ Tue, 16 Jun 2020 09:33:12: 6000000 INFO @ Tue, 16 Jun 2020 09:33:15: 3000000 INFO @ Tue, 16 Jun 2020 09:33:15: 10000000 INFO @ Tue, 16 Jun 2020 09:33:21: 7000000 INFO @ Tue, 16 Jun 2020 09:33:24: 11000000 INFO @ Tue, 16 Jun 2020 09:33:24: 4000000 INFO @ Tue, 16 Jun 2020 09:33:30: 8000000 INFO @ Tue, 16 Jun 2020 09:33:33: 12000000 INFO @ Tue, 16 Jun 2020 09:33:33: 5000000 INFO @ Tue, 16 Jun 2020 09:33:39: 9000000 INFO @ Tue, 16 Jun 2020 09:33:42: 13000000 INFO @ Tue, 16 Jun 2020 09:33:42: 6000000 INFO @ Tue, 16 Jun 2020 09:33:48: 10000000 INFO @ Tue, 16 Jun 2020 09:33:51: 14000000 INFO @ Tue, 16 Jun 2020 09:33:51: 7000000 INFO @ Tue, 16 Jun 2020 09:33:57: 11000000 INFO @ Tue, 16 Jun 2020 09:34:00: 15000000 INFO @ Tue, 16 Jun 2020 09:34:01: 8000000 INFO @ Tue, 16 Jun 2020 09:34:06: 12000000 INFO @ Tue, 16 Jun 2020 09:34:09: 16000000 INFO @ Tue, 16 Jun 2020 09:34:10: 9000000 INFO @ Tue, 16 Jun 2020 09:34:15: 13000000 INFO @ Tue, 16 Jun 2020 09:34:18: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:34:19: 10000000 INFO @ Tue, 16 Jun 2020 09:34:24: 14000000 INFO @ Tue, 16 Jun 2020 09:34:27: 18000000 INFO @ Tue, 16 Jun 2020 09:34:28: 11000000 INFO @ Tue, 16 Jun 2020 09:34:33: 15000000 INFO @ Tue, 16 Jun 2020 09:34:36: 19000000 INFO @ Tue, 16 Jun 2020 09:34:37: 12000000 INFO @ Tue, 16 Jun 2020 09:34:40: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:34:40: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:34:40: #1 total tags in treatment: 9189582 INFO @ Tue, 16 Jun 2020 09:34:40: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:34:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:34:40: #1 tags after filtering in treatment: 7670396 INFO @ Tue, 16 Jun 2020 09:34:40: #1 Redundant rate of treatment: 0.17 INFO @ Tue, 16 Jun 2020 09:34:40: #1 finished! INFO @ Tue, 16 Jun 2020 09:34:40: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:34:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:34:41: #2 number of paired peaks: 538 WARNING @ Tue, 16 Jun 2020 09:34:41: Fewer paired peaks (538) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 538 pairs to build model! INFO @ Tue, 16 Jun 2020 09:34:41: start model_add_line... INFO @ Tue, 16 Jun 2020 09:34:41: start X-correlation... INFO @ Tue, 16 Jun 2020 09:34:41: end of X-cor INFO @ Tue, 16 Jun 2020 09:34:41: #2 finished! INFO @ Tue, 16 Jun 2020 09:34:41: #2 predicted fragment length is 165 bps INFO @ Tue, 16 Jun 2020 09:34:41: #2 alternative fragment length(s) may be 4,165 bps INFO @ Tue, 16 Jun 2020 09:34:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3733160/SRX3733160.05_model.r INFO @ Tue, 16 Jun 2020 09:34:41: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:34:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:34:42: 16000000 INFO @ Tue, 16 Jun 2020 09:34:46: 13000000 INFO @ Tue, 16 Jun 2020 09:34:51: 17000000 INFO @ Tue, 16 Jun 2020 09:34:55: 14000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:34:57: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:34:59: 18000000 INFO @ Tue, 16 Jun 2020 09:35:04: 15000000 INFO @ Tue, 16 Jun 2020 09:35:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3733160/SRX3733160.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:35:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3733160/SRX3733160.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:35:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3733160/SRX3733160.05_summits.bed INFO @ Tue, 16 Jun 2020 09:35:05: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (476 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:35:08: 19000000 INFO @ Tue, 16 Jun 2020 09:35:12: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:35:12: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:35:12: #1 total tags in treatment: 9189582 INFO @ Tue, 16 Jun 2020 09:35:12: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:35:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:35:12: #1 tags after filtering in treatment: 7670396 INFO @ Tue, 16 Jun 2020 09:35:12: #1 Redundant rate of treatment: 0.17 INFO @ Tue, 16 Jun 2020 09:35:12: #1 finished! INFO @ Tue, 16 Jun 2020 09:35:12: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:35:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:35:13: #2 number of paired peaks: 538 WARNING @ Tue, 16 Jun 2020 09:35:13: Fewer paired peaks (538) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 538 pairs to build model! INFO @ Tue, 16 Jun 2020 09:35:13: start model_add_line... INFO @ Tue, 16 Jun 2020 09:35:13: start X-correlation... INFO @ Tue, 16 Jun 2020 09:35:13: 16000000 INFO @ Tue, 16 Jun 2020 09:35:13: end of X-cor INFO @ Tue, 16 Jun 2020 09:35:13: #2 finished! INFO @ Tue, 16 Jun 2020 09:35:13: #2 predicted fragment length is 165 bps INFO @ Tue, 16 Jun 2020 09:35:13: #2 alternative fragment length(s) may be 4,165 bps INFO @ Tue, 16 Jun 2020 09:35:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3733160/SRX3733160.10_model.r INFO @ Tue, 16 Jun 2020 09:35:13: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:35:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:35:21: 17000000 INFO @ Tue, 16 Jun 2020 09:35:29: 18000000 INFO @ Tue, 16 Jun 2020 09:35:29: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:35:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3733160/SRX3733160.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:35:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3733160/SRX3733160.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:35:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3733160/SRX3733160.10_summits.bed INFO @ Tue, 16 Jun 2020 09:35:37: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (347 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:35:37: 19000000 INFO @ Tue, 16 Jun 2020 09:35:40: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:35:40: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:35:40: #1 total tags in treatment: 9189582 INFO @ Tue, 16 Jun 2020 09:35:40: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:35:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:35:41: #1 tags after filtering in treatment: 7670396 INFO @ Tue, 16 Jun 2020 09:35:41: #1 Redundant rate of treatment: 0.17 INFO @ Tue, 16 Jun 2020 09:35:41: #1 finished! INFO @ Tue, 16 Jun 2020 09:35:41: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:35:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:35:41: #2 number of paired peaks: 538 WARNING @ Tue, 16 Jun 2020 09:35:41: Fewer paired peaks (538) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 538 pairs to build model! INFO @ Tue, 16 Jun 2020 09:35:41: start model_add_line... INFO @ Tue, 16 Jun 2020 09:35:41: start X-correlation... INFO @ Tue, 16 Jun 2020 09:35:41: end of X-cor INFO @ Tue, 16 Jun 2020 09:35:41: #2 finished! INFO @ Tue, 16 Jun 2020 09:35:41: #2 predicted fragment length is 165 bps INFO @ Tue, 16 Jun 2020 09:35:41: #2 alternative fragment length(s) may be 4,165 bps INFO @ Tue, 16 Jun 2020 09:35:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3733160/SRX3733160.20_model.r INFO @ Tue, 16 Jun 2020 09:35:41: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:35:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:35:57: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:36:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3733160/SRX3733160.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:36:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3733160/SRX3733160.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:36:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3733160/SRX3733160.20_summits.bed INFO @ Tue, 16 Jun 2020 09:36:05: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (231 records, 4 fields): 1 millis CompletedMACS2peakCalling