Job ID = 6507731 SRX = SRX1353668 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-26T12:50:31 prefetch.2.10.7: 1) Downloading 'SRR2722822'... 2020-06-26T12:50:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T12:52:17 prefetch.2.10.7: HTTPS download succeed 2020-06-26T12:52:17 prefetch.2.10.7: 1) 'SRR2722822' was downloaded successfully Read 14864045 spots for SRR2722822/SRR2722822.sra Written 14864045 spots for SRR2722822/SRR2722822.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:12:53 14864045 reads; of these: 14864045 (100.00%) were paired; of these: 956213 (6.43%) aligned concordantly 0 times 11857456 (79.77%) aligned concordantly exactly 1 time 2050376 (13.79%) aligned concordantly >1 times ---- 956213 pairs aligned concordantly 0 times; of these: 372724 (38.98%) aligned discordantly 1 time ---- 583489 pairs aligned 0 times concordantly or discordantly; of these: 1166978 mates make up the pairs; of these: 753092 (64.53%) aligned 0 times 257788 (22.09%) aligned exactly 1 time 156098 (13.38%) aligned >1 times 97.47% overall alignment rate Time searching: 00:12:54 Overall time: 00:12:54 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] 224924 / 14216145 = 0.0158 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 @ Fri, 26 Jun 2020 22:14:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1353668/SRX1353668.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1353668/SRX1353668.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1353668/SRX1353668.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1353668/SRX1353668.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 @ Fri, 26 Jun 2020 22:14:55: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:14:55: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:15:00: 1000000 INFO @ Fri, 26 Jun 2020 22:15:05: 2000000 INFO @ Fri, 26 Jun 2020 22:15:10: 3000000 INFO @ Fri, 26 Jun 2020 22:15:15: 4000000 INFO @ Fri, 26 Jun 2020 22:15:21: 5000000 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 @ Fri, 26 Jun 2020 22:15:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1353668/SRX1353668.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1353668/SRX1353668.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1353668/SRX1353668.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1353668/SRX1353668.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 @ Fri, 26 Jun 2020 22:15:25: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:15:25: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:15:26: 6000000 INFO @ Fri, 26 Jun 2020 22:15:31: 1000000 INFO @ Fri, 26 Jun 2020 22:15:32: 7000000 INFO @ Fri, 26 Jun 2020 22:15:38: 2000000 INFO @ Fri, 26 Jun 2020 22:15:38: 8000000 INFO @ Fri, 26 Jun 2020 22:15:44: 3000000 INFO @ Fri, 26 Jun 2020 22:15:44: 9000000 INFO @ Fri, 26 Jun 2020 22:15:50: 4000000 INFO @ Fri, 26 Jun 2020 22:15:51: 10000000 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 @ Fri, 26 Jun 2020 22:15:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1353668/SRX1353668.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1353668/SRX1353668.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1353668/SRX1353668.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1353668/SRX1353668.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 @ Fri, 26 Jun 2020 22:15:55: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:15:55: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:15:56: 5000000 INFO @ Fri, 26 Jun 2020 22:15:57: 11000000 INFO @ Fri, 26 Jun 2020 22:16:01: 1000000 INFO @ Fri, 26 Jun 2020 22:16:02: 6000000 INFO @ Fri, 26 Jun 2020 22:16:03: 12000000 INFO @ Fri, 26 Jun 2020 22:16:07: 2000000 INFO @ Fri, 26 Jun 2020 22:16:08: 7000000 INFO @ Fri, 26 Jun 2020 22:16:09: 13000000 INFO @ Fri, 26 Jun 2020 22:16:13: 3000000 INFO @ Fri, 26 Jun 2020 22:16:14: 8000000 INFO @ Fri, 26 Jun 2020 22:16:15: 14000000 INFO @ Fri, 26 Jun 2020 22:16:19: 4000000 INFO @ Fri, 26 Jun 2020 22:16:20: 9000000 INFO @ Fri, 26 Jun 2020 22:16:21: 15000000 INFO @ Fri, 26 Jun 2020 22:16:25: 5000000 INFO @ Fri, 26 Jun 2020 22:16:26: 10000000 INFO @ Fri, 26 Jun 2020 22:16:27: 16000000 INFO @ Fri, 26 Jun 2020 22:16:31: 6000000 INFO @ Fri, 26 Jun 2020 22:16:32: 11000000 INFO @ Fri, 26 Jun 2020 22:16:33: 17000000 INFO @ Fri, 26 Jun 2020 22:16:37: 7000000 INFO @ Fri, 26 Jun 2020 22:16:38: 12000000 INFO @ Fri, 26 Jun 2020 22:16:39: 18000000 INFO @ Fri, 26 Jun 2020 22:16:43: 8000000 INFO @ Fri, 26 Jun 2020 22:16:44: 13000000 INFO @ Fri, 26 Jun 2020 22:16:45: 19000000 INFO @ Fri, 26 Jun 2020 22:16:49: 9000000 INFO @ Fri, 26 Jun 2020 22:16:50: 14000000 INFO @ Fri, 26 Jun 2020 22:16:51: 20000000 INFO @ Fri, 26 Jun 2020 22:16:55: 15000000 INFO @ Fri, 26 Jun 2020 22:16:56: 10000000 INFO @ Fri, 26 Jun 2020 22:16:57: 21000000 INFO @ Fri, 26 Jun 2020 22:17:01: 16000000 INFO @ Fri, 26 Jun 2020 22:17:02: 11000000 INFO @ Fri, 26 Jun 2020 22:17:03: 22000000 INFO @ Fri, 26 Jun 2020 22:17:07: 17000000 INFO @ Fri, 26 Jun 2020 22:17:08: 12000000 INFO @ Fri, 26 Jun 2020 22:17:09: 23000000 INFO @ Fri, 26 Jun 2020 22:17:13: 18000000 INFO @ Fri, 26 Jun 2020 22:17:14: 13000000 INFO @ Fri, 26 Jun 2020 22:17:15: 24000000 INFO @ Fri, 26 Jun 2020 22:17:19: 19000000 INFO @ Fri, 26 Jun 2020 22:17:20: 14000000 INFO @ Fri, 26 Jun 2020 22:17:21: 25000000 INFO @ Fri, 26 Jun 2020 22:17:26: 20000000 INFO @ Fri, 26 Jun 2020 22:17:26: 15000000 INFO @ Fri, 26 Jun 2020 22:17:27: 26000000 INFO @ Fri, 26 Jun 2020 22:17:32: 21000000 INFO @ Fri, 26 Jun 2020 22:17:32: 16000000 INFO @ Fri, 26 Jun 2020 22:17:33: 27000000 INFO @ Fri, 26 Jun 2020 22:17:37: 22000000 INFO @ Fri, 26 Jun 2020 22:17:38: 17000000 INFO @ Fri, 26 Jun 2020 22:17:39: 28000000 INFO @ Fri, 26 Jun 2020 22:17:42: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 22:17:42: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 22:17:42: #1 total tags in treatment: 13684498 INFO @ Fri, 26 Jun 2020 22:17:42: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:17:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:17:42: #1 tags after filtering in treatment: 12708345 INFO @ Fri, 26 Jun 2020 22:17:42: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 26 Jun 2020 22:17:42: #1 finished! INFO @ Fri, 26 Jun 2020 22:17:42: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:17:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:17:43: #2 number of paired peaks: 315 WARNING @ Fri, 26 Jun 2020 22:17:43: Fewer paired peaks (315) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 315 pairs to build model! INFO @ Fri, 26 Jun 2020 22:17:43: start model_add_line... INFO @ Fri, 26 Jun 2020 22:17:43: start X-correlation... INFO @ Fri, 26 Jun 2020 22:17:43: end of X-cor INFO @ Fri, 26 Jun 2020 22:17:43: #2 finished! INFO @ Fri, 26 Jun 2020 22:17:43: #2 predicted fragment length is 133 bps INFO @ Fri, 26 Jun 2020 22:17:43: #2 alternative fragment length(s) may be 4,133 bps INFO @ Fri, 26 Jun 2020 22:17:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1353668/SRX1353668.05_model.r INFO @ Fri, 26 Jun 2020 22:17:43: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:17:43: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:17:44: 23000000 INFO @ Fri, 26 Jun 2020 22:17:44: 18000000 INFO @ Fri, 26 Jun 2020 22:17:50: 24000000 INFO @ Fri, 26 Jun 2020 22:17:50: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:17:56: 25000000 INFO @ Fri, 26 Jun 2020 22:17:56: 20000000 INFO @ Fri, 26 Jun 2020 22:18:01: 26000000 INFO @ Fri, 26 Jun 2020 22:18:02: 21000000 INFO @ Fri, 26 Jun 2020 22:18:07: 27000000 INFO @ Fri, 26 Jun 2020 22:18:08: 22000000 INFO @ Fri, 26 Jun 2020 22:18:09: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:18:13: 28000000 INFO @ Fri, 26 Jun 2020 22:18:14: 23000000 INFO @ Fri, 26 Jun 2020 22:18:16: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 22:18:16: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 22:18:16: #1 total tags in treatment: 13684498 INFO @ Fri, 26 Jun 2020 22:18:16: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:18:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:18:16: #1 tags after filtering in treatment: 12708345 INFO @ Fri, 26 Jun 2020 22:18:16: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 26 Jun 2020 22:18:16: #1 finished! INFO @ Fri, 26 Jun 2020 22:18:16: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:18:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:18:17: #2 number of paired peaks: 315 WARNING @ Fri, 26 Jun 2020 22:18:17: Fewer paired peaks (315) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 315 pairs to build model! INFO @ Fri, 26 Jun 2020 22:18:17: start model_add_line... INFO @ Fri, 26 Jun 2020 22:18:17: start X-correlation... INFO @ Fri, 26 Jun 2020 22:18:17: end of X-cor INFO @ Fri, 26 Jun 2020 22:18:17: #2 finished! INFO @ Fri, 26 Jun 2020 22:18:17: #2 predicted fragment length is 133 bps INFO @ Fri, 26 Jun 2020 22:18:17: #2 alternative fragment length(s) may be 4,133 bps INFO @ Fri, 26 Jun 2020 22:18:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1353668/SRX1353668.10_model.r INFO @ Fri, 26 Jun 2020 22:18:17: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:18:17: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:18:19: 24000000 INFO @ Fri, 26 Jun 2020 22:18:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1353668/SRX1353668.05_peaks.xls INFO @ Fri, 26 Jun 2020 22:18:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1353668/SRX1353668.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:18:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1353668/SRX1353668.05_summits.bed INFO @ Fri, 26 Jun 2020 22:18:21: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (892 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:18:25: 25000000 INFO @ Fri, 26 Jun 2020 22:18:30: 26000000 INFO @ Fri, 26 Jun 2020 22:18:36: 27000000 INFO @ Fri, 26 Jun 2020 22:18:41: 28000000 INFO @ Fri, 26 Jun 2020 22:18:42: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 22:18:44: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 22:18:44: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 22:18:44: #1 total tags in treatment: 13684498 INFO @ Fri, 26 Jun 2020 22:18:44: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:18:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:18:44: #1 tags after filtering in treatment: 12708345 INFO @ Fri, 26 Jun 2020 22:18:44: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 26 Jun 2020 22:18:44: #1 finished! INFO @ Fri, 26 Jun 2020 22:18:44: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:18:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:18:45: #2 number of paired peaks: 315 WARNING @ Fri, 26 Jun 2020 22:18:45: Fewer paired peaks (315) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 315 pairs to build model! INFO @ Fri, 26 Jun 2020 22:18:45: start model_add_line... INFO @ Fri, 26 Jun 2020 22:18:45: start X-correlation... INFO @ Fri, 26 Jun 2020 22:18:45: end of X-cor INFO @ Fri, 26 Jun 2020 22:18:45: #2 finished! INFO @ Fri, 26 Jun 2020 22:18:45: #2 predicted fragment length is 133 bps INFO @ Fri, 26 Jun 2020 22:18:45: #2 alternative fragment length(s) may be 4,133 bps INFO @ Fri, 26 Jun 2020 22:18:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1353668/SRX1353668.20_model.r INFO @ Fri, 26 Jun 2020 22:18:45: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:18:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:18:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1353668/SRX1353668.10_peaks.xls INFO @ Fri, 26 Jun 2020 22:18:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1353668/SRX1353668.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:18:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1353668/SRX1353668.10_summits.bed INFO @ Fri, 26 Jun 2020 22:18:55: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (309 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:19:11: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:19:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1353668/SRX1353668.20_peaks.xls INFO @ Fri, 26 Jun 2020 22:19:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1353668/SRX1353668.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:19:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1353668/SRX1353668.20_summits.bed INFO @ Fri, 26 Jun 2020 22:19:24: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (193 records, 4 fields): 1 millis CompletedMACS2peakCalling