Job ID = 6368453 SRX = SRX4996809 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-16T00:21:21 prefetch.2.10.7: 1) Downloading 'SRR8176695'... 2020-06-16T00:21:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:25:12 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:25:13 prefetch.2.10.7: 1) 'SRR8176695' was downloaded successfully 2020-06-16T00:25:13 prefetch.2.10.7: 'SRR8176695' has 0 unresolved dependencies Read 24332188 spots for SRR8176695/SRR8176695.sra Written 24332188 spots for SRR8176695/SRR8176695.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: 00:22:58 24332188 reads; of these: 24332188 (100.00%) were paired; of these: 2904506 (11.94%) aligned concordantly 0 times 17388109 (71.46%) aligned concordantly exactly 1 time 4039573 (16.60%) aligned concordantly >1 times ---- 2904506 pairs aligned concordantly 0 times; of these: 773878 (26.64%) aligned discordantly 1 time ---- 2130628 pairs aligned 0 times concordantly or discordantly; of these: 4261256 mates make up the pairs; of these: 3629394 (85.17%) aligned 0 times 357092 (8.38%) aligned exactly 1 time 274770 (6.45%) aligned >1 times 92.54% overall alignment rate Time searching: 00:22:58 Overall time: 00:22:58 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 20 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] 4830913 / 22188880 = 0.2177 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 10:00:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4996809/SRX4996809.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4996809/SRX4996809.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4996809/SRX4996809.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4996809/SRX4996809.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 10:00:43: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:00:43: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:00:48: 1000000 INFO @ Tue, 16 Jun 2020 10:00:52: 2000000 INFO @ Tue, 16 Jun 2020 10:00:57: 3000000 INFO @ Tue, 16 Jun 2020 10:01:01: 4000000 INFO @ Tue, 16 Jun 2020 10:01:06: 5000000 INFO @ Tue, 16 Jun 2020 10:01:10: 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 10:01:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4996809/SRX4996809.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4996809/SRX4996809.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4996809/SRX4996809.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4996809/SRX4996809.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 10:01:13: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:01:13: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:01:14: 7000000 INFO @ Tue, 16 Jun 2020 10:01:17: 1000000 INFO @ Tue, 16 Jun 2020 10:01:19: 8000000 INFO @ Tue, 16 Jun 2020 10:01:22: 2000000 INFO @ Tue, 16 Jun 2020 10:01:24: 9000000 INFO @ Tue, 16 Jun 2020 10:01:27: 3000000 INFO @ Tue, 16 Jun 2020 10:01:29: 10000000 INFO @ Tue, 16 Jun 2020 10:01:32: 4000000 INFO @ Tue, 16 Jun 2020 10:01:33: 11000000 INFO @ Tue, 16 Jun 2020 10:01:36: 5000000 INFO @ Tue, 16 Jun 2020 10:01:38: 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 10:01:41: 6000000 INFO @ Tue, 16 Jun 2020 10:01:43: 13000000 INFO @ Tue, 16 Jun 2020 10:01:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4996809/SRX4996809.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4996809/SRX4996809.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4996809/SRX4996809.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4996809/SRX4996809.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 10:01:43: #1 read tag files... INFO @ Tue, 16 Jun 2020 10:01:43: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 10:01:46: 7000000 INFO @ Tue, 16 Jun 2020 10:01:47: 14000000 INFO @ Tue, 16 Jun 2020 10:01:48: 1000000 INFO @ Tue, 16 Jun 2020 10:01:50: 8000000 INFO @ Tue, 16 Jun 2020 10:01:52: 15000000 INFO @ Tue, 16 Jun 2020 10:01:52: 2000000 INFO @ Tue, 16 Jun 2020 10:01:55: 9000000 INFO @ Tue, 16 Jun 2020 10:01:57: 16000000 INFO @ Tue, 16 Jun 2020 10:01:57: 3000000 INFO @ Tue, 16 Jun 2020 10:02:00: 10000000 INFO @ Tue, 16 Jun 2020 10:02:02: 17000000 INFO @ Tue, 16 Jun 2020 10:02:02: 4000000 INFO @ Tue, 16 Jun 2020 10:02:05: 11000000 INFO @ Tue, 16 Jun 2020 10:02:06: 18000000 INFO @ Tue, 16 Jun 2020 10:02:07: 5000000 INFO @ Tue, 16 Jun 2020 10:02:09: 12000000 INFO @ Tue, 16 Jun 2020 10:02:11: 19000000 INFO @ Tue, 16 Jun 2020 10:02:11: 6000000 INFO @ Tue, 16 Jun 2020 10:02:14: 13000000 INFO @ Tue, 16 Jun 2020 10:02:16: 20000000 INFO @ Tue, 16 Jun 2020 10:02:16: 7000000 INFO @ Tue, 16 Jun 2020 10:02:19: 14000000 INFO @ Tue, 16 Jun 2020 10:02:21: 21000000 INFO @ Tue, 16 Jun 2020 10:02:21: 8000000 INFO @ Tue, 16 Jun 2020 10:02:24: 15000000 INFO @ Tue, 16 Jun 2020 10:02:26: 22000000 INFO @ Tue, 16 Jun 2020 10:02:26: 9000000 INFO @ Tue, 16 Jun 2020 10:02:28: 16000000 INFO @ Tue, 16 Jun 2020 10:02:31: 23000000 INFO @ Tue, 16 Jun 2020 10:02:31: 10000000 INFO @ Tue, 16 Jun 2020 10:02:33: 17000000 INFO @ Tue, 16 Jun 2020 10:02:35: 24000000 INFO @ Tue, 16 Jun 2020 10:02:36: 11000000 INFO @ Tue, 16 Jun 2020 10:02:38: 18000000 INFO @ Tue, 16 Jun 2020 10:02:40: 25000000 INFO @ Tue, 16 Jun 2020 10:02:41: 12000000 INFO @ Tue, 16 Jun 2020 10:02:43: 19000000 INFO @ Tue, 16 Jun 2020 10:02:45: 26000000 INFO @ Tue, 16 Jun 2020 10:02:46: 13000000 INFO @ Tue, 16 Jun 2020 10:02:48: 20000000 INFO @ Tue, 16 Jun 2020 10:02:50: 27000000 INFO @ Tue, 16 Jun 2020 10:02:50: 14000000 INFO @ Tue, 16 Jun 2020 10:02:52: 21000000 INFO @ Tue, 16 Jun 2020 10:02:55: 28000000 INFO @ Tue, 16 Jun 2020 10:02:55: 15000000 INFO @ Tue, 16 Jun 2020 10:02:57: 22000000 INFO @ Tue, 16 Jun 2020 10:02:59: 29000000 INFO @ Tue, 16 Jun 2020 10:03:00: 16000000 INFO @ Tue, 16 Jun 2020 10:03:01: 23000000 INFO @ Tue, 16 Jun 2020 10:03:04: 30000000 INFO @ Tue, 16 Jun 2020 10:03:05: 17000000 INFO @ Tue, 16 Jun 2020 10:03:06: 24000000 INFO @ Tue, 16 Jun 2020 10:03:09: 31000000 INFO @ Tue, 16 Jun 2020 10:03:09: 18000000 INFO @ Tue, 16 Jun 2020 10:03:11: 25000000 INFO @ Tue, 16 Jun 2020 10:03:14: 19000000 INFO @ Tue, 16 Jun 2020 10:03:14: 32000000 INFO @ Tue, 16 Jun 2020 10:03:16: 26000000 INFO @ Tue, 16 Jun 2020 10:03:19: 20000000 INFO @ Tue, 16 Jun 2020 10:03:19: 33000000 INFO @ Tue, 16 Jun 2020 10:03:21: 27000000 INFO @ Tue, 16 Jun 2020 10:03:24: 21000000 INFO @ Tue, 16 Jun 2020 10:03:24: 34000000 INFO @ Tue, 16 Jun 2020 10:03:26: 28000000 INFO @ Tue, 16 Jun 2020 10:03:29: 22000000 INFO @ Tue, 16 Jun 2020 10:03:30: 35000000 INFO @ Tue, 16 Jun 2020 10:03:31: 29000000 INFO @ Tue, 16 Jun 2020 10:03:32: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 10:03:32: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 10:03:32: #1 total tags in treatment: 16663603 INFO @ Tue, 16 Jun 2020 10:03:32: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:03:32: #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 10:03:32: #1 tags after filtering in treatment: 14655441 INFO @ Tue, 16 Jun 2020 10:03:32: #1 Redundant rate of treatment: 0.12 INFO @ Tue, 16 Jun 2020 10:03:32: #1 finished! INFO @ Tue, 16 Jun 2020 10:03:32: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:03:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:03:33: #2 number of paired peaks: 481 WARNING @ Tue, 16 Jun 2020 10:03:33: Fewer paired peaks (481) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 481 pairs to build model! INFO @ Tue, 16 Jun 2020 10:03:33: start model_add_line... INFO @ Tue, 16 Jun 2020 10:03:33: start X-correlation... INFO @ Tue, 16 Jun 2020 10:03:33: end of X-cor INFO @ Tue, 16 Jun 2020 10:03:33: #2 finished! INFO @ Tue, 16 Jun 2020 10:03:33: #2 predicted fragment length is 128 bps INFO @ Tue, 16 Jun 2020 10:03:33: #2 alternative fragment length(s) may be 3,104,128 bps INFO @ Tue, 16 Jun 2020 10:03:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4996809/SRX4996809.05_model.r INFO @ Tue, 16 Jun 2020 10:03:33: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:03:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:03:34: 23000000 INFO @ Tue, 16 Jun 2020 10:03:36: 30000000 INFO @ Tue, 16 Jun 2020 10:03:39: 24000000 INFO @ Tue, 16 Jun 2020 10:03:41: 31000000 INFO @ Tue, 16 Jun 2020 10:03:44: 25000000 INFO @ Tue, 16 Jun 2020 10:03:46: 32000000 INFO @ Tue, 16 Jun 2020 10:03:49: 26000000 INFO @ Tue, 16 Jun 2020 10:03:50: 33000000 INFO @ Tue, 16 Jun 2020 10:03:54: 27000000 INFO @ Tue, 16 Jun 2020 10:03:55: 34000000 INFO @ Tue, 16 Jun 2020 10:03:59: 28000000 INFO @ Tue, 16 Jun 2020 10:04:00: 35000000 INFO @ Tue, 16 Jun 2020 10:04:02: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 10:04:02: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 10:04:02: #1 total tags in treatment: 16663603 INFO @ Tue, 16 Jun 2020 10:04:02: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:04:02: #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 10:04:03: #1 tags after filtering in treatment: 14655441 INFO @ Tue, 16 Jun 2020 10:04:03: #1 Redundant rate of treatment: 0.12 INFO @ Tue, 16 Jun 2020 10:04:03: #1 finished! INFO @ Tue, 16 Jun 2020 10:04:03: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:04:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:04:04: 29000000 INFO @ Tue, 16 Jun 2020 10:04:04: #2 number of paired peaks: 481 WARNING @ Tue, 16 Jun 2020 10:04:04: Fewer paired peaks (481) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 481 pairs to build model! INFO @ Tue, 16 Jun 2020 10:04:04: start model_add_line... INFO @ Tue, 16 Jun 2020 10:04:04: start X-correlation... INFO @ Tue, 16 Jun 2020 10:04:04: end of X-cor INFO @ Tue, 16 Jun 2020 10:04:04: #2 finished! INFO @ Tue, 16 Jun 2020 10:04:04: #2 predicted fragment length is 128 bps INFO @ Tue, 16 Jun 2020 10:04:04: #2 alternative fragment length(s) may be 3,104,128 bps INFO @ Tue, 16 Jun 2020 10:04:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4996809/SRX4996809.10_model.r INFO @ Tue, 16 Jun 2020 10:04:04: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:04:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:04:06: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 10:04:09: 30000000 INFO @ Tue, 16 Jun 2020 10:04:13: 31000000 INFO @ Tue, 16 Jun 2020 10:04:18: 32000000 INFO @ Tue, 16 Jun 2020 10:04:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4996809/SRX4996809.05_peaks.xls INFO @ Tue, 16 Jun 2020 10:04:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4996809/SRX4996809.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:04:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4996809/SRX4996809.05_summits.bed INFO @ Tue, 16 Jun 2020 10:04:23: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (496 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 10:04:23: 33000000 INFO @ Tue, 16 Jun 2020 10:04:28: 34000000 INFO @ Tue, 16 Jun 2020 10:04:33: 35000000 INFO @ Tue, 16 Jun 2020 10:04:35: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 10:04:35: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 10:04:35: #1 total tags in treatment: 16663603 INFO @ Tue, 16 Jun 2020 10:04:35: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 10:04:35: #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 10:04:35: #1 tags after filtering in treatment: 14655441 INFO @ Tue, 16 Jun 2020 10:04:35: #1 Redundant rate of treatment: 0.12 INFO @ Tue, 16 Jun 2020 10:04:35: #1 finished! INFO @ Tue, 16 Jun 2020 10:04:35: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 10:04:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 10:04:36: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:04:36: #2 number of paired peaks: 481 WARNING @ Tue, 16 Jun 2020 10:04:36: Fewer paired peaks (481) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 481 pairs to build model! INFO @ Tue, 16 Jun 2020 10:04:36: start model_add_line... INFO @ Tue, 16 Jun 2020 10:04:36: start X-correlation... INFO @ Tue, 16 Jun 2020 10:04:36: end of X-cor INFO @ Tue, 16 Jun 2020 10:04:36: #2 finished! INFO @ Tue, 16 Jun 2020 10:04:36: #2 predicted fragment length is 128 bps INFO @ Tue, 16 Jun 2020 10:04:36: #2 alternative fragment length(s) may be 3,104,128 bps INFO @ Tue, 16 Jun 2020 10:04:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4996809/SRX4996809.20_model.r INFO @ Tue, 16 Jun 2020 10:04:36: #3 Call peaks... INFO @ Tue, 16 Jun 2020 10:04:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 10:04:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4996809/SRX4996809.10_peaks.xls INFO @ Tue, 16 Jun 2020 10:04:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4996809/SRX4996809.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:04:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4996809/SRX4996809.10_summits.bed INFO @ Tue, 16 Jun 2020 10:04:52: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (368 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 10:05:08: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 10:05:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4996809/SRX4996809.20_peaks.xls INFO @ Tue, 16 Jun 2020 10:05:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4996809/SRX4996809.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 10:05:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4996809/SRX4996809.20_summits.bed INFO @ Tue, 16 Jun 2020 10:05:25: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (240 records, 4 fields): 1 millis CompletedMACS2peakCalling