Job ID = 6497343 SRX = SRX1353668 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-25T22:31:49 prefetch.2.10.7: 1) Downloading 'SRR2722822'... 2020-06-25T22:31:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:34:24 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:34:24 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:14:30 14864045 reads; of these: 14864045 (100.00%) were paired; of these: 956388 (6.43%) aligned concordantly 0 times 11857434 (79.77%) aligned concordantly exactly 1 time 2050223 (13.79%) aligned concordantly >1 times ---- 956388 pairs aligned concordantly 0 times; of these: 372701 (38.97%) aligned discordantly 1 time ---- 583687 pairs aligned 0 times concordantly or discordantly; of these: 1167374 mates make up the pairs; of these: 753437 (64.54%) aligned 0 times 257825 (22.09%) aligned exactly 1 time 156112 (13.37%) aligned >1 times 97.47% overall alignment rate Time searching: 00:14:30 Overall time: 00:14:30 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] 224917 / 14215953 = 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 07:59:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1353668/SRX1353668.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1353668/SRX1353668.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1353668/SRX1353668.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/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 07:59:56: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:59:56: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:00:02: 1000000 INFO @ Fri, 26 Jun 2020 08:00:08: 2000000 INFO @ Fri, 26 Jun 2020 08:00:13: 3000000 INFO @ Fri, 26 Jun 2020 08:00:19: 4000000 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 08:00:25: 5000000 INFO @ Fri, 26 Jun 2020 08:00:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1353668/SRX1353668.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1353668/SRX1353668.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1353668/SRX1353668.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/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 08:00:26: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:00:26: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:00:32: 6000000 INFO @ Fri, 26 Jun 2020 08:00:34: 1000000 INFO @ Fri, 26 Jun 2020 08:00:39: 7000000 INFO @ Fri, 26 Jun 2020 08:00:42: 2000000 INFO @ Fri, 26 Jun 2020 08:00:46: 8000000 INFO @ Fri, 26 Jun 2020 08:00:50: 3000000 INFO @ Fri, 26 Jun 2020 08:00:53: 9000000 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 08:00:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1353668/SRX1353668.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1353668/SRX1353668.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1353668/SRX1353668.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/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 08:00:56: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:00:56: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:00:58: 4000000 INFO @ Fri, 26 Jun 2020 08:01:01: 10000000 INFO @ Fri, 26 Jun 2020 08:01:03: 1000000 INFO @ Fri, 26 Jun 2020 08:01:07: 5000000 INFO @ Fri, 26 Jun 2020 08:01:08: 11000000 INFO @ Fri, 26 Jun 2020 08:01:11: 2000000 INFO @ Fri, 26 Jun 2020 08:01:15: 6000000 INFO @ Fri, 26 Jun 2020 08:01:16: 12000000 INFO @ Fri, 26 Jun 2020 08:01:18: 3000000 INFO @ Fri, 26 Jun 2020 08:01:23: 7000000 INFO @ Fri, 26 Jun 2020 08:01:23: 13000000 INFO @ Fri, 26 Jun 2020 08:01:26: 4000000 INFO @ Fri, 26 Jun 2020 08:01:31: 14000000 INFO @ Fri, 26 Jun 2020 08:01:32: 8000000 INFO @ Fri, 26 Jun 2020 08:01:33: 5000000 INFO @ Fri, 26 Jun 2020 08:01:38: 15000000 INFO @ Fri, 26 Jun 2020 08:01:40: 9000000 INFO @ Fri, 26 Jun 2020 08:01:41: 6000000 INFO @ Fri, 26 Jun 2020 08:01:46: 16000000 INFO @ Fri, 26 Jun 2020 08:01:48: 7000000 INFO @ Fri, 26 Jun 2020 08:01:49: 10000000 INFO @ Fri, 26 Jun 2020 08:01:53: 17000000 INFO @ Fri, 26 Jun 2020 08:01:56: 8000000 INFO @ Fri, 26 Jun 2020 08:01:57: 11000000 INFO @ Fri, 26 Jun 2020 08:02:01: 18000000 INFO @ Fri, 26 Jun 2020 08:02:03: 9000000 INFO @ Fri, 26 Jun 2020 08:02:05: 12000000 INFO @ Fri, 26 Jun 2020 08:02:08: 19000000 INFO @ Fri, 26 Jun 2020 08:02:11: 10000000 INFO @ Fri, 26 Jun 2020 08:02:13: 13000000 INFO @ Fri, 26 Jun 2020 08:02:16: 20000000 INFO @ Fri, 26 Jun 2020 08:02:19: 11000000 INFO @ Fri, 26 Jun 2020 08:02:21: 14000000 INFO @ Fri, 26 Jun 2020 08:02:23: 21000000 INFO @ Fri, 26 Jun 2020 08:02:26: 12000000 INFO @ Fri, 26 Jun 2020 08:02:29: 15000000 INFO @ Fri, 26 Jun 2020 08:02:31: 22000000 INFO @ Fri, 26 Jun 2020 08:02:33: 13000000 INFO @ Fri, 26 Jun 2020 08:02:37: 16000000 INFO @ Fri, 26 Jun 2020 08:02:38: 23000000 INFO @ Fri, 26 Jun 2020 08:02:41: 14000000 INFO @ Fri, 26 Jun 2020 08:02:45: 24000000 INFO @ Fri, 26 Jun 2020 08:02:45: 17000000 INFO @ Fri, 26 Jun 2020 08:02:48: 15000000 INFO @ Fri, 26 Jun 2020 08:02:52: 25000000 INFO @ Fri, 26 Jun 2020 08:02:53: 18000000 INFO @ Fri, 26 Jun 2020 08:02:56: 16000000 INFO @ Fri, 26 Jun 2020 08:02:59: 26000000 INFO @ Fri, 26 Jun 2020 08:03:01: 19000000 INFO @ Fri, 26 Jun 2020 08:03:04: 17000000 INFO @ Fri, 26 Jun 2020 08:03:06: 27000000 INFO @ Fri, 26 Jun 2020 08:03:09: 20000000 INFO @ Fri, 26 Jun 2020 08:03:11: 18000000 INFO @ Fri, 26 Jun 2020 08:03:14: 28000000 INFO @ Fri, 26 Jun 2020 08:03:17: 21000000 INFO @ Fri, 26 Jun 2020 08:03:17: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:03:17: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:03:17: #1 total tags in treatment: 13684329 INFO @ Fri, 26 Jun 2020 08:03:17: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:03:17: #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 08:03:18: #1 tags after filtering in treatment: 12708268 INFO @ Fri, 26 Jun 2020 08:03:18: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 26 Jun 2020 08:03:18: #1 finished! INFO @ Fri, 26 Jun 2020 08:03:18: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:03:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:03:19: #2 number of paired peaks: 315 WARNING @ Fri, 26 Jun 2020 08:03:19: 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 08:03:19: start model_add_line... INFO @ Fri, 26 Jun 2020 08:03:19: 19000000 INFO @ Fri, 26 Jun 2020 08:03:19: start X-correlation... INFO @ Fri, 26 Jun 2020 08:03:19: end of X-cor INFO @ Fri, 26 Jun 2020 08:03:19: #2 finished! INFO @ Fri, 26 Jun 2020 08:03:19: #2 predicted fragment length is 132 bps INFO @ Fri, 26 Jun 2020 08:03:19: #2 alternative fragment length(s) may be 4,132 bps INFO @ Fri, 26 Jun 2020 08:03:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1353668/SRX1353668.05_model.r INFO @ Fri, 26 Jun 2020 08:03:19: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:03:19: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 08:03:25: 22000000 INFO @ Fri, 26 Jun 2020 08:03:26: 20000000 INFO @ Fri, 26 Jun 2020 08:03:33: 23000000 INFO @ Fri, 26 Jun 2020 08:03:34: 21000000 INFO @ Fri, 26 Jun 2020 08:03:41: 24000000 INFO @ Fri, 26 Jun 2020 08:03:41: 22000000 INFO @ Fri, 26 Jun 2020 08:03:49: 25000000 INFO @ Fri, 26 Jun 2020 08:03:49: 23000000 INFO @ Fri, 26 Jun 2020 08:03:49: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:03:57: 24000000 INFO @ Fri, 26 Jun 2020 08:03:57: 26000000 INFO @ Fri, 26 Jun 2020 08:04:04: 25000000 INFO @ Fri, 26 Jun 2020 08:04:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1353668/SRX1353668.05_peaks.xls INFO @ Fri, 26 Jun 2020 08:04:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1353668/SRX1353668.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:04:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1353668/SRX1353668.05_summits.bed INFO @ Fri, 26 Jun 2020 08:04:05: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (891 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:04:05: 27000000 INFO @ Fri, 26 Jun 2020 08:04:12: 26000000 INFO @ Fri, 26 Jun 2020 08:04:13: 28000000 INFO @ Fri, 26 Jun 2020 08:04:17: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:04:17: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:04:17: #1 total tags in treatment: 13684329 INFO @ Fri, 26 Jun 2020 08:04:17: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:04:17: #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 08:04:17: #1 tags after filtering in treatment: 12708268 INFO @ Fri, 26 Jun 2020 08:04:17: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 26 Jun 2020 08:04:17: #1 finished! INFO @ Fri, 26 Jun 2020 08:04:17: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:04:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:04:18: #2 number of paired peaks: 315 WARNING @ Fri, 26 Jun 2020 08:04:18: 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 08:04:18: start model_add_line... INFO @ Fri, 26 Jun 2020 08:04:18: start X-correlation... INFO @ Fri, 26 Jun 2020 08:04:18: end of X-cor INFO @ Fri, 26 Jun 2020 08:04:18: #2 finished! INFO @ Fri, 26 Jun 2020 08:04:18: #2 predicted fragment length is 132 bps INFO @ Fri, 26 Jun 2020 08:04:18: #2 alternative fragment length(s) may be 4,132 bps INFO @ Fri, 26 Jun 2020 08:04:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1353668/SRX1353668.10_model.r INFO @ Fri, 26 Jun 2020 08:04:18: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:04:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:04:19: 27000000 BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 08:04:25: 28000000 INFO @ Fri, 26 Jun 2020 08:04:28: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:04:28: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:04:28: #1 total tags in treatment: 13684329 INFO @ Fri, 26 Jun 2020 08:04:28: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:04:28: #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 08:04:29: #1 tags after filtering in treatment: 12708268 INFO @ Fri, 26 Jun 2020 08:04:29: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 26 Jun 2020 08:04:29: #1 finished! INFO @ Fri, 26 Jun 2020 08:04:29: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:04:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:04:29: #2 number of paired peaks: 315 WARNING @ Fri, 26 Jun 2020 08:04:29: 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 08:04:29: start model_add_line... INFO @ Fri, 26 Jun 2020 08:04:30: start X-correlation... INFO @ Fri, 26 Jun 2020 08:04:30: end of X-cor INFO @ Fri, 26 Jun 2020 08:04:30: #2 finished! INFO @ Fri, 26 Jun 2020 08:04:30: #2 predicted fragment length is 132 bps INFO @ Fri, 26 Jun 2020 08:04:30: #2 alternative fragment length(s) may be 4,132 bps INFO @ Fri, 26 Jun 2020 08:04:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1353668/SRX1353668.20_model.r INFO @ Fri, 26 Jun 2020 08:04:30: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:04:30: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:04:49: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:04:59: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:05:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1353668/SRX1353668.10_peaks.xls INFO @ Fri, 26 Jun 2020 08:05:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1353668/SRX1353668.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:05:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1353668/SRX1353668.10_summits.bed INFO @ Fri, 26 Jun 2020 08:05:03: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (304 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:05:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1353668/SRX1353668.20_peaks.xls INFO @ Fri, 26 Jun 2020 08:05:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1353668/SRX1353668.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:05:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1353668/SRX1353668.20_summits.bed INFO @ Fri, 26 Jun 2020 08:05:15: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (193 records, 4 fields): 2 millis CompletedMACS2peakCalling