Job ID = 6367790 SRX = SRX4085358 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T23:44:44 prefetch.2.10.7: 1) Downloading 'SRR7167387'... 2020-06-15T23:44:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:52:50 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:52:50 prefetch.2.10.7: 1) 'SRR7167387' was downloaded successfully Read 24365244 spots for SRR7167387/SRR7167387.sra Written 24365244 spots for SRR7167387/SRR7167387.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: 00:20:44 24365244 reads; of these: 24365244 (100.00%) were paired; of these: 858771 (3.52%) aligned concordantly 0 times 20471253 (84.02%) aligned concordantly exactly 1 time 3035220 (12.46%) aligned concordantly >1 times ---- 858771 pairs aligned concordantly 0 times; of these: 114227 (13.30%) aligned discordantly 1 time ---- 744544 pairs aligned 0 times concordantly or discordantly; of these: 1489088 mates make up the pairs; of these: 856034 (57.49%) aligned 0 times 494265 (33.19%) aligned exactly 1 time 138789 (9.32%) aligned >1 times 98.24% overall alignment rate Time searching: 00:20:44 Overall time: 00:20:44 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] 4140070 / 23570506 = 0.1756 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 09:28:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085358/SRX4085358.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085358/SRX4085358.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085358/SRX4085358.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085358/SRX4085358.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 09:28:34: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:28:34: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:28:40: 1000000 INFO @ Tue, 16 Jun 2020 09:28:46: 2000000 INFO @ Tue, 16 Jun 2020 09:28:52: 3000000 INFO @ Tue, 16 Jun 2020 09:28:58: 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 @ Tue, 16 Jun 2020 09:29:04: 5000000 INFO @ Tue, 16 Jun 2020 09:29:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085358/SRX4085358.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085358/SRX4085358.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085358/SRX4085358.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085358/SRX4085358.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 09:29:04: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:29:04: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:29:10: 6000000 INFO @ Tue, 16 Jun 2020 09:29:11: 1000000 INFO @ Tue, 16 Jun 2020 09:29:17: 7000000 INFO @ Tue, 16 Jun 2020 09:29:18: 2000000 INFO @ Tue, 16 Jun 2020 09:29:23: 8000000 INFO @ Tue, 16 Jun 2020 09:29:24: 3000000 INFO @ Tue, 16 Jun 2020 09:29:30: 9000000 INFO @ Tue, 16 Jun 2020 09:29:31: 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 @ Tue, 16 Jun 2020 09:29:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085358/SRX4085358.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085358/SRX4085358.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085358/SRX4085358.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085358/SRX4085358.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 09:29:34: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:29:34: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:29:36: 10000000 INFO @ Tue, 16 Jun 2020 09:29:37: 5000000 INFO @ Tue, 16 Jun 2020 09:29:41: 1000000 INFO @ Tue, 16 Jun 2020 09:29:43: 11000000 INFO @ Tue, 16 Jun 2020 09:29:44: 6000000 INFO @ Tue, 16 Jun 2020 09:29:47: 2000000 INFO @ Tue, 16 Jun 2020 09:29:49: 12000000 INFO @ Tue, 16 Jun 2020 09:29:51: 7000000 INFO @ Tue, 16 Jun 2020 09:29:54: 3000000 INFO @ Tue, 16 Jun 2020 09:29:56: 13000000 INFO @ Tue, 16 Jun 2020 09:29:57: 8000000 INFO @ Tue, 16 Jun 2020 09:30:00: 4000000 INFO @ Tue, 16 Jun 2020 09:30:02: 14000000 INFO @ Tue, 16 Jun 2020 09:30:04: 9000000 INFO @ Tue, 16 Jun 2020 09:30:07: 5000000 INFO @ Tue, 16 Jun 2020 09:30:08: 15000000 INFO @ Tue, 16 Jun 2020 09:30:10: 10000000 INFO @ Tue, 16 Jun 2020 09:30:13: 6000000 INFO @ Tue, 16 Jun 2020 09:30:15: 16000000 INFO @ Tue, 16 Jun 2020 09:30:17: 11000000 INFO @ Tue, 16 Jun 2020 09:30:20: 7000000 INFO @ Tue, 16 Jun 2020 09:30:21: 17000000 INFO @ Tue, 16 Jun 2020 09:30:23: 12000000 INFO @ Tue, 16 Jun 2020 09:30:26: 8000000 INFO @ Tue, 16 Jun 2020 09:30:28: 18000000 INFO @ Tue, 16 Jun 2020 09:30:30: 13000000 INFO @ Tue, 16 Jun 2020 09:30:32: 9000000 INFO @ Tue, 16 Jun 2020 09:30:34: 19000000 INFO @ Tue, 16 Jun 2020 09:30:36: 14000000 INFO @ Tue, 16 Jun 2020 09:30:39: 10000000 INFO @ Tue, 16 Jun 2020 09:30:40: 20000000 INFO @ Tue, 16 Jun 2020 09:30:43: 15000000 INFO @ Tue, 16 Jun 2020 09:30:45: 11000000 INFO @ Tue, 16 Jun 2020 09:30:46: 21000000 INFO @ Tue, 16 Jun 2020 09:30:49: 16000000 INFO @ Tue, 16 Jun 2020 09:30:52: 12000000 INFO @ Tue, 16 Jun 2020 09:30:53: 22000000 INFO @ Tue, 16 Jun 2020 09:30:56: 17000000 INFO @ Tue, 16 Jun 2020 09:30:58: 13000000 INFO @ Tue, 16 Jun 2020 09:30:59: 23000000 INFO @ Tue, 16 Jun 2020 09:31:02: 18000000 INFO @ Tue, 16 Jun 2020 09:31:05: 14000000 INFO @ Tue, 16 Jun 2020 09:31:06: 24000000 INFO @ Tue, 16 Jun 2020 09:31:09: 19000000 INFO @ Tue, 16 Jun 2020 09:31:11: 15000000 INFO @ Tue, 16 Jun 2020 09:31:12: 25000000 INFO @ Tue, 16 Jun 2020 09:31:15: 20000000 INFO @ Tue, 16 Jun 2020 09:31:17: 16000000 INFO @ Tue, 16 Jun 2020 09:31:18: 26000000 INFO @ Tue, 16 Jun 2020 09:31:22: 21000000 INFO @ Tue, 16 Jun 2020 09:31:24: 17000000 INFO @ Tue, 16 Jun 2020 09:31:25: 27000000 INFO @ Tue, 16 Jun 2020 09:31:29: 22000000 INFO @ Tue, 16 Jun 2020 09:31:30: 18000000 INFO @ Tue, 16 Jun 2020 09:31:31: 28000000 INFO @ Tue, 16 Jun 2020 09:31:35: 23000000 INFO @ Tue, 16 Jun 2020 09:31:37: 19000000 INFO @ Tue, 16 Jun 2020 09:31:37: 29000000 INFO @ Tue, 16 Jun 2020 09:31:42: 24000000 INFO @ Tue, 16 Jun 2020 09:31:43: 20000000 INFO @ Tue, 16 Jun 2020 09:31:44: 30000000 INFO @ Tue, 16 Jun 2020 09:31:48: 25000000 INFO @ Tue, 16 Jun 2020 09:31:50: 21000000 INFO @ Tue, 16 Jun 2020 09:31:50: 31000000 INFO @ Tue, 16 Jun 2020 09:31:55: 26000000 INFO @ Tue, 16 Jun 2020 09:31:56: 22000000 INFO @ Tue, 16 Jun 2020 09:31:56: 32000000 INFO @ Tue, 16 Jun 2020 09:32:01: 27000000 INFO @ Tue, 16 Jun 2020 09:32:03: 23000000 INFO @ Tue, 16 Jun 2020 09:32:03: 33000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:32:08: 28000000 INFO @ Tue, 16 Jun 2020 09:32:09: 34000000 INFO @ Tue, 16 Jun 2020 09:32:09: 24000000 INFO @ Tue, 16 Jun 2020 09:32:14: 29000000 INFO @ Tue, 16 Jun 2020 09:32:15: 35000000 INFO @ Tue, 16 Jun 2020 09:32:15: 25000000 INFO @ Tue, 16 Jun 2020 09:32:21: 30000000 INFO @ Tue, 16 Jun 2020 09:32:22: 36000000 INFO @ Tue, 16 Jun 2020 09:32:22: 26000000 INFO @ Tue, 16 Jun 2020 09:32:27: 31000000 INFO @ Tue, 16 Jun 2020 09:32:28: 37000000 INFO @ Tue, 16 Jun 2020 09:32:28: 27000000 INFO @ Tue, 16 Jun 2020 09:32:34: 32000000 INFO @ Tue, 16 Jun 2020 09:32:34: 38000000 INFO @ Tue, 16 Jun 2020 09:32:35: 28000000 INFO @ Tue, 16 Jun 2020 09:32:40: 33000000 INFO @ Tue, 16 Jun 2020 09:32:41: 39000000 INFO @ Tue, 16 Jun 2020 09:32:41: 29000000 INFO @ Tue, 16 Jun 2020 09:32:44: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:32:44: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:32:44: #1 total tags in treatment: 19377225 INFO @ Tue, 16 Jun 2020 09:32:44: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:32:44: #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 09:32:45: #1 tags after filtering in treatment: 15675025 INFO @ Tue, 16 Jun 2020 09:32:45: #1 Redundant rate of treatment: 0.19 INFO @ Tue, 16 Jun 2020 09:32:45: #1 finished! INFO @ Tue, 16 Jun 2020 09:32:45: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:32:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:32:46: #2 number of paired peaks: 204 WARNING @ Tue, 16 Jun 2020 09:32:46: Fewer paired peaks (204) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 204 pairs to build model! INFO @ Tue, 16 Jun 2020 09:32:46: start model_add_line... INFO @ Tue, 16 Jun 2020 09:32:46: start X-correlation... INFO @ Tue, 16 Jun 2020 09:32:46: end of X-cor INFO @ Tue, 16 Jun 2020 09:32:46: #2 finished! INFO @ Tue, 16 Jun 2020 09:32:46: #2 predicted fragment length is 103 bps INFO @ Tue, 16 Jun 2020 09:32:46: #2 alternative fragment length(s) may be 2,103 bps INFO @ Tue, 16 Jun 2020 09:32:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085358/SRX4085358.05_model.r INFO @ Tue, 16 Jun 2020 09:32:46: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:32:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:32:47: 34000000 INFO @ Tue, 16 Jun 2020 09:32:48: 30000000 INFO @ Tue, 16 Jun 2020 09:32:53: 35000000 INFO @ Tue, 16 Jun 2020 09:32:54: 31000000 INFO @ Tue, 16 Jun 2020 09:32:59: 36000000 INFO @ Tue, 16 Jun 2020 09:33:00: 32000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:33:06: 37000000 INFO @ Tue, 16 Jun 2020 09:33:06: 33000000 INFO @ Tue, 16 Jun 2020 09:33:12: 38000000 INFO @ Tue, 16 Jun 2020 09:33:12: 34000000 INFO @ Tue, 16 Jun 2020 09:33:12: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:33:18: 39000000 INFO @ Tue, 16 Jun 2020 09:33:18: 35000000 INFO @ Tue, 16 Jun 2020 09:33:22: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:33:22: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:33:22: #1 total tags in treatment: 19377225 INFO @ Tue, 16 Jun 2020 09:33:22: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:33:22: #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 09:33:22: #1 tags after filtering in treatment: 15675025 INFO @ Tue, 16 Jun 2020 09:33:22: #1 Redundant rate of treatment: 0.19 INFO @ Tue, 16 Jun 2020 09:33:22: #1 finished! INFO @ Tue, 16 Jun 2020 09:33:22: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:33:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:33:23: #2 number of paired peaks: 204 WARNING @ Tue, 16 Jun 2020 09:33:23: Fewer paired peaks (204) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 204 pairs to build model! INFO @ Tue, 16 Jun 2020 09:33:23: start model_add_line... INFO @ Tue, 16 Jun 2020 09:33:23: start X-correlation... INFO @ Tue, 16 Jun 2020 09:33:23: end of X-cor INFO @ Tue, 16 Jun 2020 09:33:23: #2 finished! INFO @ Tue, 16 Jun 2020 09:33:23: #2 predicted fragment length is 103 bps INFO @ Tue, 16 Jun 2020 09:33:23: #2 alternative fragment length(s) may be 2,103 bps INFO @ Tue, 16 Jun 2020 09:33:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085358/SRX4085358.10_model.r INFO @ Tue, 16 Jun 2020 09:33:23: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:33:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:33:24: 36000000 INFO @ Tue, 16 Jun 2020 09:33:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085358/SRX4085358.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:33:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085358/SRX4085358.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:33:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085358/SRX4085358.05_summits.bed INFO @ Tue, 16 Jun 2020 09:33:26: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1952 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:33:30: 37000000 INFO @ Tue, 16 Jun 2020 09:33:36: 38000000 INFO @ Tue, 16 Jun 2020 09:33:41: 39000000 INFO @ Tue, 16 Jun 2020 09:33:44: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:33:44: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:33:44: #1 total tags in treatment: 19377225 INFO @ Tue, 16 Jun 2020 09:33:44: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:33:44: #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 09:33:45: #1 tags after filtering in treatment: 15675025 INFO @ Tue, 16 Jun 2020 09:33:45: #1 Redundant rate of treatment: 0.19 INFO @ Tue, 16 Jun 2020 09:33:45: #1 finished! INFO @ Tue, 16 Jun 2020 09:33:45: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:33:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:33:46: #2 number of paired peaks: 204 WARNING @ Tue, 16 Jun 2020 09:33:46: Fewer paired peaks (204) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 204 pairs to build model! INFO @ Tue, 16 Jun 2020 09:33:46: start model_add_line... INFO @ Tue, 16 Jun 2020 09:33:46: start X-correlation... INFO @ Tue, 16 Jun 2020 09:33:46: end of X-cor INFO @ Tue, 16 Jun 2020 09:33:46: #2 finished! INFO @ Tue, 16 Jun 2020 09:33:46: #2 predicted fragment length is 103 bps INFO @ Tue, 16 Jun 2020 09:33:46: #2 alternative fragment length(s) may be 2,103 bps INFO @ Tue, 16 Jun 2020 09:33:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085358/SRX4085358.20_model.r INFO @ Tue, 16 Jun 2020 09:33:46: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:33:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:33:50: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:34:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085358/SRX4085358.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:34:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085358/SRX4085358.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:34:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085358/SRX4085358.10_summits.bed INFO @ Tue, 16 Jun 2020 09:34:03: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (988 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:34:13: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:34:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085358/SRX4085358.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:34:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085358/SRX4085358.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:34:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085358/SRX4085358.20_summits.bed INFO @ Tue, 16 Jun 2020 09:34:27: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (393 records, 4 fields): 1 millis CompletedMACS2peakCalling