Job ID = 6497337 SRX = SRX1353664 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-25T21:58:25 prefetch.2.10.7: 1) Downloading 'SRR2722818'... 2020-06-25T21:58:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:01:56 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:01:56 prefetch.2.10.7: 1) 'SRR2722818' was downloaded successfully Read 15191543 spots for SRR2722818/SRR2722818.sra Written 15191543 spots for SRR2722818/SRR2722818.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: 00:00:01 Multiseed full-index search: 00:17:16 15191543 reads; of these: 15191543 (100.00%) were paired; of these: 971486 (6.39%) aligned concordantly 0 times 11699495 (77.01%) aligned concordantly exactly 1 time 2520562 (16.59%) aligned concordantly >1 times ---- 971486 pairs aligned concordantly 0 times; of these: 505764 (52.06%) aligned discordantly 1 time ---- 465722 pairs aligned 0 times concordantly or discordantly; of these: 931444 mates make up the pairs; of these: 490713 (52.68%) aligned 0 times 221214 (23.75%) aligned exactly 1 time 219517 (23.57%) aligned >1 times 98.38% overall alignment rate Time searching: 00:17:18 Overall time: 00:17:18 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 16 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] 637145 / 14692468 = 0.0434 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 07:32:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1353664/SRX1353664.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1353664/SRX1353664.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1353664/SRX1353664.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1353664/SRX1353664.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 07:32:58: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:32:58: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:33:04: 1000000 INFO @ Fri, 26 Jun 2020 07:33:10: 2000000 INFO @ Fri, 26 Jun 2020 07:33:16: 3000000 INFO @ Fri, 26 Jun 2020 07:33:21: 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 07:33:27: 5000000 INFO @ Fri, 26 Jun 2020 07:33:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1353664/SRX1353664.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1353664/SRX1353664.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1353664/SRX1353664.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1353664/SRX1353664.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 07:33:28: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:33:28: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:33:34: 6000000 INFO @ Fri, 26 Jun 2020 07:33:35: 1000000 INFO @ Fri, 26 Jun 2020 07:33:40: 7000000 INFO @ Fri, 26 Jun 2020 07:33:42: 2000000 INFO @ Fri, 26 Jun 2020 07:33:47: 8000000 INFO @ Fri, 26 Jun 2020 07:33:49: 3000000 INFO @ Fri, 26 Jun 2020 07:33:54: 9000000 INFO @ Fri, 26 Jun 2020 07:33:56: 4000000 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 07:33:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1353664/SRX1353664.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1353664/SRX1353664.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1353664/SRX1353664.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1353664/SRX1353664.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 07:33:58: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:33:58: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:34:02: 10000000 INFO @ Fri, 26 Jun 2020 07:34:04: 5000000 INFO @ Fri, 26 Jun 2020 07:34:07: 1000000 INFO @ Fri, 26 Jun 2020 07:34:11: 11000000 INFO @ Fri, 26 Jun 2020 07:34:13: 6000000 INFO @ Fri, 26 Jun 2020 07:34:17: 2000000 INFO @ Fri, 26 Jun 2020 07:34:20: 12000000 INFO @ Fri, 26 Jun 2020 07:34:22: 7000000 INFO @ Fri, 26 Jun 2020 07:34:27: 3000000 INFO @ Fri, 26 Jun 2020 07:34:28: 13000000 INFO @ Fri, 26 Jun 2020 07:34:30: 8000000 INFO @ Fri, 26 Jun 2020 07:34:36: 4000000 INFO @ Fri, 26 Jun 2020 07:34:37: 14000000 INFO @ Fri, 26 Jun 2020 07:34:39: 9000000 INFO @ Fri, 26 Jun 2020 07:34:45: 15000000 INFO @ Fri, 26 Jun 2020 07:34:45: 5000000 INFO @ Fri, 26 Jun 2020 07:34:47: 10000000 INFO @ Fri, 26 Jun 2020 07:34:53: 16000000 INFO @ Fri, 26 Jun 2020 07:34:54: 6000000 INFO @ Fri, 26 Jun 2020 07:34:55: 11000000 INFO @ Fri, 26 Jun 2020 07:35:02: 17000000 INFO @ Fri, 26 Jun 2020 07:35:04: 12000000 INFO @ Fri, 26 Jun 2020 07:35:04: 7000000 INFO @ Fri, 26 Jun 2020 07:35:10: 18000000 INFO @ Fri, 26 Jun 2020 07:35:12: 13000000 INFO @ Fri, 26 Jun 2020 07:35:13: 8000000 INFO @ Fri, 26 Jun 2020 07:35:19: 19000000 INFO @ Fri, 26 Jun 2020 07:35:20: 14000000 INFO @ Fri, 26 Jun 2020 07:35:22: 9000000 INFO @ Fri, 26 Jun 2020 07:35:27: 20000000 INFO @ Fri, 26 Jun 2020 07:35:29: 15000000 INFO @ Fri, 26 Jun 2020 07:35:31: 10000000 INFO @ Fri, 26 Jun 2020 07:35:35: 21000000 INFO @ Fri, 26 Jun 2020 07:35:37: 16000000 INFO @ Fri, 26 Jun 2020 07:35:40: 11000000 INFO @ Fri, 26 Jun 2020 07:35:44: 22000000 INFO @ Fri, 26 Jun 2020 07:35:45: 17000000 INFO @ Fri, 26 Jun 2020 07:35:50: 12000000 INFO @ Fri, 26 Jun 2020 07:35:53: 23000000 INFO @ Fri, 26 Jun 2020 07:35:55: 18000000 INFO @ Fri, 26 Jun 2020 07:36:01: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:36:06: 24000000 INFO @ Fri, 26 Jun 2020 07:36:08: 19000000 INFO @ Fri, 26 Jun 2020 07:36:13: 14000000 INFO @ Fri, 26 Jun 2020 07:36:16: 25000000 INFO @ Fri, 26 Jun 2020 07:36:17: 20000000 INFO @ Fri, 26 Jun 2020 07:36:23: 15000000 INFO @ Fri, 26 Jun 2020 07:36:25: 26000000 INFO @ Fri, 26 Jun 2020 07:36:26: 21000000 INFO @ Fri, 26 Jun 2020 07:36:33: 16000000 INFO @ Fri, 26 Jun 2020 07:36:33: 27000000 INFO @ Fri, 26 Jun 2020 07:36:34: 22000000 INFO @ Fri, 26 Jun 2020 07:36:41: 28000000 INFO @ Fri, 26 Jun 2020 07:36:42: 17000000 INFO @ Fri, 26 Jun 2020 07:36:42: 23000000 INFO @ Fri, 26 Jun 2020 07:36:46: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:36:46: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:36:46: #1 total tags in treatment: 13590583 INFO @ Fri, 26 Jun 2020 07:36:46: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:36:46: #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 07:36:47: #1 tags after filtering in treatment: 12416663 INFO @ Fri, 26 Jun 2020 07:36:47: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 26 Jun 2020 07:36:47: #1 finished! INFO @ Fri, 26 Jun 2020 07:36:47: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:36:47: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:36:48: #2 number of paired peaks: 407 WARNING @ Fri, 26 Jun 2020 07:36:48: Fewer paired peaks (407) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 407 pairs to build model! INFO @ Fri, 26 Jun 2020 07:36:48: start model_add_line... INFO @ Fri, 26 Jun 2020 07:36:48: start X-correlation... INFO @ Fri, 26 Jun 2020 07:36:48: end of X-cor INFO @ Fri, 26 Jun 2020 07:36:48: #2 finished! INFO @ Fri, 26 Jun 2020 07:36:48: #2 predicted fragment length is 143 bps INFO @ Fri, 26 Jun 2020 07:36:48: #2 alternative fragment length(s) may be 4,143 bps INFO @ Fri, 26 Jun 2020 07:36:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1353664/SRX1353664.05_model.r INFO @ Fri, 26 Jun 2020 07:36:48: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:36:48: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:36:51: 24000000 INFO @ Fri, 26 Jun 2020 07:36:52: 18000000 INFO @ Fri, 26 Jun 2020 07:36:59: 25000000 INFO @ Fri, 26 Jun 2020 07:37:01: 19000000 BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:37:07: 26000000 INFO @ Fri, 26 Jun 2020 07:37:11: 20000000 INFO @ Fri, 26 Jun 2020 07:37:16: 27000000 INFO @ Fri, 26 Jun 2020 07:37:17: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:37:20: 21000000 INFO @ Fri, 26 Jun 2020 07:37:24: 28000000 INFO @ Fri, 26 Jun 2020 07:37:29: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:37:29: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:37:29: #1 total tags in treatment: 13590583 INFO @ Fri, 26 Jun 2020 07:37:29: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:37:29: #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 07:37:29: #1 tags after filtering in treatment: 12416663 INFO @ Fri, 26 Jun 2020 07:37:29: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 26 Jun 2020 07:37:29: #1 finished! INFO @ Fri, 26 Jun 2020 07:37:29: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:37:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:37:30: 22000000 INFO @ Fri, 26 Jun 2020 07:37:30: #2 number of paired peaks: 407 WARNING @ Fri, 26 Jun 2020 07:37:30: Fewer paired peaks (407) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 407 pairs to build model! INFO @ Fri, 26 Jun 2020 07:37:30: start model_add_line... INFO @ Fri, 26 Jun 2020 07:37:30: start X-correlation... INFO @ Fri, 26 Jun 2020 07:37:30: end of X-cor INFO @ Fri, 26 Jun 2020 07:37:30: #2 finished! INFO @ Fri, 26 Jun 2020 07:37:30: #2 predicted fragment length is 143 bps INFO @ Fri, 26 Jun 2020 07:37:30: #2 alternative fragment length(s) may be 4,143 bps INFO @ Fri, 26 Jun 2020 07:37:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1353664/SRX1353664.10_model.r INFO @ Fri, 26 Jun 2020 07:37:30: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:37:30: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:37:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1353664/SRX1353664.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:37:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1353664/SRX1353664.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:37:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1353664/SRX1353664.05_summits.bed INFO @ Fri, 26 Jun 2020 07:37:32: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (402 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:37:38: 23000000 INFO @ Fri, 26 Jun 2020 07:37:46: 24000000 INFO @ Fri, 26 Jun 2020 07:37:55: 25000000 INFO @ Fri, 26 Jun 2020 07:38:00: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:38:03: 26000000 INFO @ Fri, 26 Jun 2020 07:38:12: 27000000 INFO @ Fri, 26 Jun 2020 07:38:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1353664/SRX1353664.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:38:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1353664/SRX1353664.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:38:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1353664/SRX1353664.10_summits.bed INFO @ Fri, 26 Jun 2020 07:38:15: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (288 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:38:20: 28000000 INFO @ Fri, 26 Jun 2020 07:38:25: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:38:25: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:38:25: #1 total tags in treatment: 13590583 INFO @ Fri, 26 Jun 2020 07:38:25: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:38:25: #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 07:38:25: #1 tags after filtering in treatment: 12416663 INFO @ Fri, 26 Jun 2020 07:38:25: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 26 Jun 2020 07:38:25: #1 finished! INFO @ Fri, 26 Jun 2020 07:38:25: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:38:25: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:38:26: #2 number of paired peaks: 407 WARNING @ Fri, 26 Jun 2020 07:38:26: Fewer paired peaks (407) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 407 pairs to build model! INFO @ Fri, 26 Jun 2020 07:38:26: start model_add_line... INFO @ Fri, 26 Jun 2020 07:38:26: start X-correlation... INFO @ Fri, 26 Jun 2020 07:38:26: end of X-cor INFO @ Fri, 26 Jun 2020 07:38:26: #2 finished! INFO @ Fri, 26 Jun 2020 07:38:26: #2 predicted fragment length is 143 bps INFO @ Fri, 26 Jun 2020 07:38:26: #2 alternative fragment length(s) may be 4,143 bps INFO @ Fri, 26 Jun 2020 07:38:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1353664/SRX1353664.20_model.r INFO @ Fri, 26 Jun 2020 07:38:26: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:38:26: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:38:58: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:39:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1353664/SRX1353664.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:39:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1353664/SRX1353664.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:39:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1353664/SRX1353664.20_summits.bed INFO @ Fri, 26 Jun 2020 07:39:13: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (209 records, 4 fields): 1 millis CompletedMACS2peakCalling