Job ID = 6497386 SRX = SRX4085366 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-25T21:46:03 prefetch.2.10.7: 1) Downloading 'SRR7167395'... 2020-06-25T21:46:28 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T21:51:19 prefetch.2.10.7: HTTPS download succeed 2020-06-25T21:51:19 prefetch.2.10.7: 1) 'SRR7167395' was downloaded successfully Read 25802778 spots for SRR7167395/SRR7167395.sra Written 25802778 spots for SRR7167395/SRR7167395.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: 00:20:27 25802778 reads; of these: 25802778 (100.00%) were paired; of these: 8088976 (31.35%) aligned concordantly 0 times 15209356 (58.94%) aligned concordantly exactly 1 time 2504446 (9.71%) aligned concordantly >1 times ---- 8088976 pairs aligned concordantly 0 times; of these: 221217 (2.73%) aligned discordantly 1 time ---- 7867759 pairs aligned 0 times concordantly or discordantly; of these: 15735518 mates make up the pairs; of these: 13069161 (83.06%) aligned 0 times 2299384 (14.61%) aligned exactly 1 time 366973 (2.33%) aligned >1 times 74.67% overall alignment rate Time searching: 00:20:27 Overall time: 00:20:27 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] 4846550 / 17851598 = 0.2715 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 07:25:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4085366/SRX4085366.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4085366/SRX4085366.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4085366/SRX4085366.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4085366/SRX4085366.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 07:25:58: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:25:58: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:26:04: 1000000 INFO @ Fri, 26 Jun 2020 07:26:09: 2000000 INFO @ Fri, 26 Jun 2020 07:26:15: 3000000 INFO @ Fri, 26 Jun 2020 07:26:20: 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 07:26:26: 5000000 INFO @ Fri, 26 Jun 2020 07:26:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4085366/SRX4085366.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4085366/SRX4085366.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4085366/SRX4085366.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4085366/SRX4085366.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 07:26:28: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:26:28: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:26:32: 6000000 INFO @ Fri, 26 Jun 2020 07:26:35: 1000000 INFO @ Fri, 26 Jun 2020 07:26:38: 7000000 INFO @ Fri, 26 Jun 2020 07:26:41: 2000000 INFO @ Fri, 26 Jun 2020 07:26:44: 8000000 INFO @ Fri, 26 Jun 2020 07:26:48: 3000000 INFO @ Fri, 26 Jun 2020 07:26:51: 9000000 INFO @ Fri, 26 Jun 2020 07:26:55: 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 07:26:57: 10000000 INFO @ Fri, 26 Jun 2020 07:26:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4085366/SRX4085366.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4085366/SRX4085366.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4085366/SRX4085366.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4085366/SRX4085366.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 07:26:58: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:26:58: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:27:02: 5000000 INFO @ Fri, 26 Jun 2020 07:27:03: 11000000 INFO @ Fri, 26 Jun 2020 07:27:04: 1000000 INFO @ Fri, 26 Jun 2020 07:27:08: 6000000 INFO @ Fri, 26 Jun 2020 07:27:10: 12000000 INFO @ Fri, 26 Jun 2020 07:27:11: 2000000 INFO @ Fri, 26 Jun 2020 07:27:15: 7000000 INFO @ Fri, 26 Jun 2020 07:27:16: 13000000 INFO @ Fri, 26 Jun 2020 07:27:17: 3000000 INFO @ Fri, 26 Jun 2020 07:27:22: 8000000 INFO @ Fri, 26 Jun 2020 07:27:23: 14000000 INFO @ Fri, 26 Jun 2020 07:27:23: 4000000 INFO @ Fri, 26 Jun 2020 07:27:29: 15000000 INFO @ Fri, 26 Jun 2020 07:27:29: 9000000 INFO @ Fri, 26 Jun 2020 07:27:29: 5000000 INFO @ Fri, 26 Jun 2020 07:27:35: 16000000 INFO @ Fri, 26 Jun 2020 07:27:36: 6000000 INFO @ Fri, 26 Jun 2020 07:27:36: 10000000 INFO @ Fri, 26 Jun 2020 07:27:41: 17000000 INFO @ Fri, 26 Jun 2020 07:27:42: 7000000 INFO @ Fri, 26 Jun 2020 07:27:43: 11000000 INFO @ Fri, 26 Jun 2020 07:27:47: 18000000 INFO @ Fri, 26 Jun 2020 07:27:48: 8000000 INFO @ Fri, 26 Jun 2020 07:27:50: 12000000 INFO @ Fri, 26 Jun 2020 07:27:54: 19000000 INFO @ Fri, 26 Jun 2020 07:27:55: 9000000 INFO @ Fri, 26 Jun 2020 07:27:57: 13000000 INFO @ Fri, 26 Jun 2020 07:28:00: 20000000 INFO @ Fri, 26 Jun 2020 07:28:01: 10000000 INFO @ Fri, 26 Jun 2020 07:28:04: 14000000 INFO @ Fri, 26 Jun 2020 07:28:07: 21000000 INFO @ Fri, 26 Jun 2020 07:28:07: 11000000 INFO @ Fri, 26 Jun 2020 07:28:11: 15000000 INFO @ Fri, 26 Jun 2020 07:28:13: 22000000 INFO @ Fri, 26 Jun 2020 07:28:14: 12000000 INFO @ Fri, 26 Jun 2020 07:28:18: 16000000 INFO @ Fri, 26 Jun 2020 07:28:19: 23000000 INFO @ Fri, 26 Jun 2020 07:28:20: 13000000 INFO @ Fri, 26 Jun 2020 07:28:24: 17000000 INFO @ Fri, 26 Jun 2020 07:28:26: 24000000 INFO @ Fri, 26 Jun 2020 07:28:26: 14000000 INFO @ Fri, 26 Jun 2020 07:28:31: 18000000 INFO @ Fri, 26 Jun 2020 07:28:32: 25000000 INFO @ Fri, 26 Jun 2020 07:28:33: 15000000 INFO @ Fri, 26 Jun 2020 07:28:38: 19000000 INFO @ Fri, 26 Jun 2020 07:28:38: 26000000 INFO @ Fri, 26 Jun 2020 07:28:39: 16000000 INFO @ Fri, 26 Jun 2020 07:28:44: 27000000 INFO @ Fri, 26 Jun 2020 07:28:45: 20000000 INFO @ Fri, 26 Jun 2020 07:28:45: 17000000 INFO @ Fri, 26 Jun 2020 07:28:51: 28000000 INFO @ Fri, 26 Jun 2020 07:28:51: 18000000 INFO @ Fri, 26 Jun 2020 07:28:52: 21000000 INFO @ Fri, 26 Jun 2020 07:28:56: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 07:28:56: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 07:28:56: #1 total tags in treatment: 12901941 INFO @ Fri, 26 Jun 2020 07:28:56: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:28:56: #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 07:28:56: #1 tags after filtering in treatment: 11759313 INFO @ Fri, 26 Jun 2020 07:28:56: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 26 Jun 2020 07:28:56: #1 finished! INFO @ Fri, 26 Jun 2020 07:28:56: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:28:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:28:57: 19000000 INFO @ Fri, 26 Jun 2020 07:28:57: #2 number of paired peaks: 311 WARNING @ Fri, 26 Jun 2020 07:28:57: Fewer paired peaks (311) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 311 pairs to build model! INFO @ Fri, 26 Jun 2020 07:28:57: start model_add_line... INFO @ Fri, 26 Jun 2020 07:28:57: start X-correlation... INFO @ Fri, 26 Jun 2020 07:28:57: end of X-cor INFO @ Fri, 26 Jun 2020 07:28:57: #2 finished! INFO @ Fri, 26 Jun 2020 07:28:57: #2 predicted fragment length is 119 bps INFO @ Fri, 26 Jun 2020 07:28:57: #2 alternative fragment length(s) may be 4,119 bps INFO @ Fri, 26 Jun 2020 07:28:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4085366/SRX4085366.05_model.r INFO @ Fri, 26 Jun 2020 07:28:57: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:28:57: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:28:58: 22000000 INFO @ Fri, 26 Jun 2020 07:29:03: 20000000 INFO @ Fri, 26 Jun 2020 07:29:05: 23000000 INFO @ Fri, 26 Jun 2020 07:29:10: 21000000 INFO @ Fri, 26 Jun 2020 07:29:12: 24000000 INFO @ Fri, 26 Jun 2020 07:29:16: 22000000 INFO @ Fri, 26 Jun 2020 07:29:19: 25000000 INFO @ Fri, 26 Jun 2020 07:29:22: 23000000 INFO @ Fri, 26 Jun 2020 07:29:22: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:29:25: 26000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:29:28: 24000000 INFO @ Fri, 26 Jun 2020 07:29:32: 27000000 INFO @ Fri, 26 Jun 2020 07:29:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4085366/SRX4085366.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:29:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4085366/SRX4085366.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:29:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4085366/SRX4085366.05_summits.bed INFO @ Fri, 26 Jun 2020 07:29:34: Done! INFO @ Fri, 26 Jun 2020 07:29:34: 25000000 pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (978 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:29:39: 28000000 INFO @ Fri, 26 Jun 2020 07:29:40: 26000000 INFO @ Fri, 26 Jun 2020 07:29:44: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 07:29:44: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 07:29:44: #1 total tags in treatment: 12901941 INFO @ Fri, 26 Jun 2020 07:29:44: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:29:44: #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 07:29:44: #1 tags after filtering in treatment: 11759313 INFO @ Fri, 26 Jun 2020 07:29:44: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 26 Jun 2020 07:29:44: #1 finished! INFO @ Fri, 26 Jun 2020 07:29:44: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:29:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:29:45: #2 number of paired peaks: 311 WARNING @ Fri, 26 Jun 2020 07:29:45: Fewer paired peaks (311) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 311 pairs to build model! INFO @ Fri, 26 Jun 2020 07:29:45: start model_add_line... INFO @ Fri, 26 Jun 2020 07:29:45: start X-correlation... INFO @ Fri, 26 Jun 2020 07:29:45: end of X-cor INFO @ Fri, 26 Jun 2020 07:29:45: #2 finished! INFO @ Fri, 26 Jun 2020 07:29:45: #2 predicted fragment length is 119 bps INFO @ Fri, 26 Jun 2020 07:29:45: #2 alternative fragment length(s) may be 4,119 bps INFO @ Fri, 26 Jun 2020 07:29:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4085366/SRX4085366.10_model.r INFO @ Fri, 26 Jun 2020 07:29:45: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:29:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:29:46: 27000000 INFO @ Fri, 26 Jun 2020 07:29:52: 28000000 INFO @ Fri, 26 Jun 2020 07:29:57: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 07:29:57: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 07:29:57: #1 total tags in treatment: 12901941 INFO @ Fri, 26 Jun 2020 07:29:57: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:29:57: #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 07:29:57: #1 tags after filtering in treatment: 11759313 INFO @ Fri, 26 Jun 2020 07:29:57: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 26 Jun 2020 07:29:57: #1 finished! INFO @ Fri, 26 Jun 2020 07:29:57: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:29:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:29:58: #2 number of paired peaks: 311 WARNING @ Fri, 26 Jun 2020 07:29:58: Fewer paired peaks (311) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 311 pairs to build model! INFO @ Fri, 26 Jun 2020 07:29:58: start model_add_line... INFO @ Fri, 26 Jun 2020 07:29:58: start X-correlation... INFO @ Fri, 26 Jun 2020 07:29:58: end of X-cor INFO @ Fri, 26 Jun 2020 07:29:58: #2 finished! INFO @ Fri, 26 Jun 2020 07:29:58: #2 predicted fragment length is 119 bps INFO @ Fri, 26 Jun 2020 07:29:58: #2 alternative fragment length(s) may be 4,119 bps INFO @ Fri, 26 Jun 2020 07:29:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4085366/SRX4085366.20_model.r INFO @ Fri, 26 Jun 2020 07:29:58: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:29:58: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:30:10: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:30:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4085366/SRX4085366.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:30:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4085366/SRX4085366.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:30:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4085366/SRX4085366.10_summits.bed INFO @ Fri, 26 Jun 2020 07:30:22: Done! INFO @ Fri, 26 Jun 2020 07:30:22: #3 Call peaks for each chromosome... pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (566 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:30:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4085366/SRX4085366.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:30:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4085366/SRX4085366.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:30:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4085366/SRX4085366.20_summits.bed INFO @ Fri, 26 Jun 2020 07:30:33: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (290 records, 4 fields): 1 millis CompletedMACS2peakCalling