Job ID = 6366360 SRX = SRX1353659 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T22:53:26 prefetch.2.10.7: 1) Downloading 'SRR2722813'... 2020-06-15T22:53:26 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:55:02 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:55:02 prefetch.2.10.7: 1) 'SRR2722813' was downloaded successfully Read 14134670 spots for SRR2722813/SRR2722813.sra Written 14134670 spots for SRR2722813/SRR2722813.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: 00:12:53 14134670 reads; of these: 14134670 (100.00%) were paired; of these: 590368 (4.18%) aligned concordantly 0 times 11499534 (81.36%) aligned concordantly exactly 1 time 2044768 (14.47%) aligned concordantly >1 times ---- 590368 pairs aligned concordantly 0 times; of these: 316147 (53.55%) aligned discordantly 1 time ---- 274221 pairs aligned 0 times concordantly or discordantly; of these: 548442 mates make up the pairs; of these: 240166 (43.79%) aligned 0 times 167803 (30.60%) aligned exactly 1 time 140473 (25.61%) aligned >1 times 99.15% overall alignment rate Time searching: 00:12:53 Overall time: 00:12:53 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] 175207 / 13719726 = 0.0128 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 08:17:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1353659/SRX1353659.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1353659/SRX1353659.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1353659/SRX1353659.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1353659/SRX1353659.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 08:17:55: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:17:55: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:18:00: 1000000 INFO @ Tue, 16 Jun 2020 08:18:05: 2000000 INFO @ Tue, 16 Jun 2020 08:18:09: 3000000 INFO @ Tue, 16 Jun 2020 08:18:14: 4000000 INFO @ Tue, 16 Jun 2020 08:18:18: 5000000 INFO @ Tue, 16 Jun 2020 08:18:23: 6000000 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 08:18:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1353659/SRX1353659.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1353659/SRX1353659.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1353659/SRX1353659.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1353659/SRX1353659.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 08:18:25: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:18:25: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:18:27: 7000000 INFO @ Tue, 16 Jun 2020 08:18:30: 1000000 INFO @ Tue, 16 Jun 2020 08:18:32: 8000000 INFO @ Tue, 16 Jun 2020 08:18:35: 2000000 INFO @ Tue, 16 Jun 2020 08:18:37: 9000000 INFO @ Tue, 16 Jun 2020 08:18:40: 3000000 INFO @ Tue, 16 Jun 2020 08:18:41: 10000000 INFO @ Tue, 16 Jun 2020 08:18:44: 4000000 INFO @ Tue, 16 Jun 2020 08:18:46: 11000000 INFO @ Tue, 16 Jun 2020 08:18:49: 5000000 INFO @ Tue, 16 Jun 2020 08:18:50: 12000000 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 08:18:53: 6000000 INFO @ Tue, 16 Jun 2020 08:18:55: 13000000 INFO @ Tue, 16 Jun 2020 08:18:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1353659/SRX1353659.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1353659/SRX1353659.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1353659/SRX1353659.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1353659/SRX1353659.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 08:18:55: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:18:55: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:18:58: 7000000 INFO @ Tue, 16 Jun 2020 08:19:00: 14000000 INFO @ Tue, 16 Jun 2020 08:19:00: 1000000 INFO @ Tue, 16 Jun 2020 08:19:03: 8000000 INFO @ Tue, 16 Jun 2020 08:19:04: 15000000 INFO @ Tue, 16 Jun 2020 08:19:05: 2000000 INFO @ Tue, 16 Jun 2020 08:19:08: 9000000 INFO @ Tue, 16 Jun 2020 08:19:09: 16000000 INFO @ Tue, 16 Jun 2020 08:19:09: 3000000 INFO @ Tue, 16 Jun 2020 08:19:12: 10000000 INFO @ Tue, 16 Jun 2020 08:19:13: 17000000 INFO @ Tue, 16 Jun 2020 08:19:14: 4000000 INFO @ Tue, 16 Jun 2020 08:19:17: 11000000 INFO @ Tue, 16 Jun 2020 08:19:18: 18000000 INFO @ Tue, 16 Jun 2020 08:19:19: 5000000 INFO @ Tue, 16 Jun 2020 08:19:22: 12000000 INFO @ Tue, 16 Jun 2020 08:19:23: 19000000 INFO @ Tue, 16 Jun 2020 08:19:23: 6000000 INFO @ Tue, 16 Jun 2020 08:19:26: 13000000 INFO @ Tue, 16 Jun 2020 08:19:27: 20000000 INFO @ Tue, 16 Jun 2020 08:19:28: 7000000 INFO @ Tue, 16 Jun 2020 08:19:31: 14000000 INFO @ Tue, 16 Jun 2020 08:19:32: 21000000 INFO @ Tue, 16 Jun 2020 08:19:33: 8000000 INFO @ Tue, 16 Jun 2020 08:19:36: 15000000 INFO @ Tue, 16 Jun 2020 08:19:37: 22000000 INFO @ Tue, 16 Jun 2020 08:19:37: 9000000 INFO @ Tue, 16 Jun 2020 08:19:41: 16000000 INFO @ Tue, 16 Jun 2020 08:19:41: 23000000 INFO @ Tue, 16 Jun 2020 08:19:42: 10000000 INFO @ Tue, 16 Jun 2020 08:19:46: 17000000 INFO @ Tue, 16 Jun 2020 08:19:46: 24000000 INFO @ Tue, 16 Jun 2020 08:19:47: 11000000 INFO @ Tue, 16 Jun 2020 08:19:51: 25000000 INFO @ Tue, 16 Jun 2020 08:19:51: 18000000 INFO @ Tue, 16 Jun 2020 08:19:51: 12000000 INFO @ Tue, 16 Jun 2020 08:19:55: 26000000 INFO @ Tue, 16 Jun 2020 08:19:56: 19000000 INFO @ Tue, 16 Jun 2020 08:19:56: 13000000 INFO @ Tue, 16 Jun 2020 08:20:00: 27000000 INFO @ Tue, 16 Jun 2020 08:20:01: 20000000 INFO @ Tue, 16 Jun 2020 08:20:01: 14000000 INFO @ Tue, 16 Jun 2020 08:20:03: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:20:03: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:20:03: #1 total tags in treatment: 13369863 INFO @ Tue, 16 Jun 2020 08:20:03: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:20:03: #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 08:20:04: #1 tags after filtering in treatment: 12272866 INFO @ Tue, 16 Jun 2020 08:20:04: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 16 Jun 2020 08:20:04: #1 finished! INFO @ Tue, 16 Jun 2020 08:20:04: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:20:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:20:05: #2 number of paired peaks: 337 WARNING @ Tue, 16 Jun 2020 08:20:05: Fewer paired peaks (337) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 337 pairs to build model! INFO @ Tue, 16 Jun 2020 08:20:05: start model_add_line... INFO @ Tue, 16 Jun 2020 08:20:05: start X-correlation... INFO @ Tue, 16 Jun 2020 08:20:05: end of X-cor INFO @ Tue, 16 Jun 2020 08:20:05: #2 finished! INFO @ Tue, 16 Jun 2020 08:20:05: #2 predicted fragment length is 120 bps INFO @ Tue, 16 Jun 2020 08:20:05: #2 alternative fragment length(s) may be 4,120,143 bps INFO @ Tue, 16 Jun 2020 08:20:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1353659/SRX1353659.05_model.r INFO @ Tue, 16 Jun 2020 08:20:05: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:20:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:20:05: 15000000 INFO @ Tue, 16 Jun 2020 08:20:05: 21000000 INFO @ Tue, 16 Jun 2020 08:20:10: 16000000 INFO @ Tue, 16 Jun 2020 08:20:10: 22000000 INFO @ Tue, 16 Jun 2020 08:20:15: 17000000 INFO @ Tue, 16 Jun 2020 08:20:15: 23000000 INFO @ Tue, 16 Jun 2020 08:20:19: 18000000 INFO @ Tue, 16 Jun 2020 08:20:20: 24000000 INFO @ Tue, 16 Jun 2020 08:20:24: 19000000 INFO @ Tue, 16 Jun 2020 08:20:25: 25000000 INFO @ Tue, 16 Jun 2020 08:20:29: 20000000 INFO @ Tue, 16 Jun 2020 08:20:30: 26000000 INFO @ Tue, 16 Jun 2020 08:20:30: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:20:33: 21000000 INFO @ Tue, 16 Jun 2020 08:20:35: 27000000 INFO @ Tue, 16 Jun 2020 08:20:38: 22000000 INFO @ Tue, 16 Jun 2020 08:20:38: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:20:38: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:20:38: #1 total tags in treatment: 13369863 INFO @ Tue, 16 Jun 2020 08:20:38: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:20:38: #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 08:20:38: #1 tags after filtering in treatment: 12272866 INFO @ Tue, 16 Jun 2020 08:20:38: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 16 Jun 2020 08:20:38: #1 finished! INFO @ Tue, 16 Jun 2020 08:20:38: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:20:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:20:39: #2 number of paired peaks: 337 WARNING @ Tue, 16 Jun 2020 08:20:39: Fewer paired peaks (337) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 337 pairs to build model! INFO @ Tue, 16 Jun 2020 08:20:39: start model_add_line... INFO @ Tue, 16 Jun 2020 08:20:39: start X-correlation... INFO @ Tue, 16 Jun 2020 08:20:39: end of X-cor INFO @ Tue, 16 Jun 2020 08:20:39: #2 finished! INFO @ Tue, 16 Jun 2020 08:20:39: #2 predicted fragment length is 120 bps INFO @ Tue, 16 Jun 2020 08:20:39: #2 alternative fragment length(s) may be 4,120,143 bps INFO @ Tue, 16 Jun 2020 08:20:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1353659/SRX1353659.10_model.r INFO @ Tue, 16 Jun 2020 08:20:39: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:20:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:20:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1353659/SRX1353659.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:20:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1353659/SRX1353659.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:20:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1353659/SRX1353659.05_summits.bed INFO @ Tue, 16 Jun 2020 08:20:42: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (594 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:20:43: 23000000 INFO @ Tue, 16 Jun 2020 08:20:47: 24000000 INFO @ Tue, 16 Jun 2020 08:20:52: 25000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:20:56: 26000000 INFO @ Tue, 16 Jun 2020 08:21:01: 27000000 INFO @ Tue, 16 Jun 2020 08:21:04: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:21:04: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:21:04: #1 total tags in treatment: 13369863 INFO @ Tue, 16 Jun 2020 08:21:04: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:21:04: #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 08:21:04: #1 tags after filtering in treatment: 12272866 INFO @ Tue, 16 Jun 2020 08:21:04: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 16 Jun 2020 08:21:04: #1 finished! INFO @ Tue, 16 Jun 2020 08:21:04: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:21:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:21:05: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:21:05: #2 number of paired peaks: 337 WARNING @ Tue, 16 Jun 2020 08:21:05: Fewer paired peaks (337) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 337 pairs to build model! INFO @ Tue, 16 Jun 2020 08:21:05: start model_add_line... INFO @ Tue, 16 Jun 2020 08:21:05: start X-correlation... INFO @ Tue, 16 Jun 2020 08:21:05: end of X-cor INFO @ Tue, 16 Jun 2020 08:21:05: #2 finished! INFO @ Tue, 16 Jun 2020 08:21:05: #2 predicted fragment length is 120 bps INFO @ Tue, 16 Jun 2020 08:21:05: #2 alternative fragment length(s) may be 4,120,143 bps INFO @ Tue, 16 Jun 2020 08:21:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1353659/SRX1353659.20_model.r INFO @ Tue, 16 Jun 2020 08:21:05: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:21:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:21:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1353659/SRX1353659.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:21:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1353659/SRX1353659.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:21:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1353659/SRX1353659.10_summits.bed INFO @ Tue, 16 Jun 2020 08:21:18: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (313 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:21:30: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:21:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1353659/SRX1353659.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:21:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1353659/SRX1353659.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:21:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1353659/SRX1353659.20_summits.bed INFO @ Tue, 16 Jun 2020 08:21:42: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (195 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。