Job ID = 6367871 SRX = SRX4085438 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T23:41:14 prefetch.2.10.7: 1) Downloading 'SRR7167467'... 2020-06-15T23:41:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:46:40 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:46:40 prefetch.2.10.7: 1) 'SRR7167467' was downloaded successfully Read 21680904 spots for SRR7167467/SRR7167467.sra Written 21680904 spots for SRR7167467/SRR7167467.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: 00:13:45 21680904 reads; of these: 21680904 (100.00%) were paired; of these: 9299618 (42.89%) aligned concordantly 0 times 9826185 (45.32%) aligned concordantly exactly 1 time 2555101 (11.79%) aligned concordantly >1 times ---- 9299618 pairs aligned concordantly 0 times; of these: 179374 (1.93%) aligned discordantly 1 time ---- 9120244 pairs aligned 0 times concordantly or discordantly; of these: 18240488 mates make up the pairs; of these: 15032202 (82.41%) aligned 0 times 2803355 (15.37%) aligned exactly 1 time 404931 (2.22%) aligned >1 times 65.33% overall alignment rate Time searching: 00:13:45 Overall time: 00:13:45 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] 1941208 / 12498045 = 0.1553 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 09:10:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085438/SRX4085438.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085438/SRX4085438.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085438/SRX4085438.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085438/SRX4085438.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 09:10:04: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:10:04: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:10:10: 1000000 INFO @ Tue, 16 Jun 2020 09:10:16: 2000000 INFO @ Tue, 16 Jun 2020 09:10:22: 3000000 INFO @ Tue, 16 Jun 2020 09:10:28: 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 09:10:34: 5000000 INFO @ Tue, 16 Jun 2020 09:10:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085438/SRX4085438.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085438/SRX4085438.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085438/SRX4085438.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085438/SRX4085438.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 09:10:34: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:10:34: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:10:41: 6000000 INFO @ Tue, 16 Jun 2020 09:10:41: 1000000 INFO @ Tue, 16 Jun 2020 09:10:48: 7000000 INFO @ Tue, 16 Jun 2020 09:10:49: 2000000 INFO @ Tue, 16 Jun 2020 09:10:55: 8000000 INFO @ Tue, 16 Jun 2020 09:10:57: 3000000 INFO @ Tue, 16 Jun 2020 09:11:02: 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 @ Tue, 16 Jun 2020 09:11:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085438/SRX4085438.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085438/SRX4085438.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085438/SRX4085438.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085438/SRX4085438.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 09:11:04: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:11:04: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:11:04: 4000000 INFO @ Tue, 16 Jun 2020 09:11:09: 10000000 INFO @ Tue, 16 Jun 2020 09:11:11: 1000000 INFO @ Tue, 16 Jun 2020 09:11:12: 5000000 INFO @ Tue, 16 Jun 2020 09:11:16: 11000000 INFO @ Tue, 16 Jun 2020 09:11:18: 2000000 INFO @ Tue, 16 Jun 2020 09:11:20: 6000000 INFO @ Tue, 16 Jun 2020 09:11:23: 12000000 INFO @ Tue, 16 Jun 2020 09:11:25: 3000000 INFO @ Tue, 16 Jun 2020 09:11:28: 7000000 INFO @ Tue, 16 Jun 2020 09:11:30: 13000000 INFO @ Tue, 16 Jun 2020 09:11:33: 4000000 INFO @ Tue, 16 Jun 2020 09:11:37: 8000000 INFO @ Tue, 16 Jun 2020 09:11:38: 14000000 INFO @ Tue, 16 Jun 2020 09:11:40: 5000000 INFO @ Tue, 16 Jun 2020 09:11:45: 9000000 INFO @ Tue, 16 Jun 2020 09:11:45: 15000000 INFO @ Tue, 16 Jun 2020 09:11:47: 6000000 INFO @ Tue, 16 Jun 2020 09:11:52: 16000000 INFO @ Tue, 16 Jun 2020 09:11:53: 10000000 INFO @ Tue, 16 Jun 2020 09:11:54: 7000000 INFO @ Tue, 16 Jun 2020 09:12:00: 17000000 INFO @ Tue, 16 Jun 2020 09:12:01: 11000000 INFO @ Tue, 16 Jun 2020 09:12:02: 8000000 INFO @ Tue, 16 Jun 2020 09:12:07: 18000000 INFO @ Tue, 16 Jun 2020 09:12:09: 9000000 INFO @ Tue, 16 Jun 2020 09:12:09: 12000000 INFO @ Tue, 16 Jun 2020 09:12:14: 19000000 INFO @ Tue, 16 Jun 2020 09:12:16: 10000000 INFO @ Tue, 16 Jun 2020 09:12:17: 13000000 INFO @ Tue, 16 Jun 2020 09:12:22: 20000000 INFO @ Tue, 16 Jun 2020 09:12:23: 11000000 INFO @ Tue, 16 Jun 2020 09:12:25: 14000000 INFO @ Tue, 16 Jun 2020 09:12:29: 21000000 INFO @ Tue, 16 Jun 2020 09:12:31: 12000000 INFO @ Tue, 16 Jun 2020 09:12:33: 15000000 INFO @ Tue, 16 Jun 2020 09:12:37: 22000000 INFO @ Tue, 16 Jun 2020 09:12:38: 13000000 INFO @ Tue, 16 Jun 2020 09:12:41: 16000000 INFO @ Tue, 16 Jun 2020 09:12:44: 23000000 INFO @ Tue, 16 Jun 2020 09:12:46: 14000000 INFO @ Tue, 16 Jun 2020 09:12:49: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:12:51: 24000000 INFO @ Tue, 16 Jun 2020 09:12:53: 15000000 INFO @ Tue, 16 Jun 2020 09:12:54: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:12:54: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:12:54: #1 total tags in treatment: 10452053 INFO @ Tue, 16 Jun 2020 09:12:54: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:12:54: #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 09:12:54: #1 tags after filtering in treatment: 8625845 INFO @ Tue, 16 Jun 2020 09:12:54: #1 Redundant rate of treatment: 0.17 INFO @ Tue, 16 Jun 2020 09:12:54: #1 finished! INFO @ Tue, 16 Jun 2020 09:12:54: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:12:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:12:55: #2 number of paired peaks: 533 WARNING @ Tue, 16 Jun 2020 09:12:55: Fewer paired peaks (533) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 533 pairs to build model! INFO @ Tue, 16 Jun 2020 09:12:55: start model_add_line... INFO @ Tue, 16 Jun 2020 09:12:55: start X-correlation... INFO @ Tue, 16 Jun 2020 09:12:55: end of X-cor INFO @ Tue, 16 Jun 2020 09:12:55: #2 finished! INFO @ Tue, 16 Jun 2020 09:12:55: #2 predicted fragment length is 107 bps INFO @ Tue, 16 Jun 2020 09:12:55: #2 alternative fragment length(s) may be 107 bps INFO @ Tue, 16 Jun 2020 09:12:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085438/SRX4085438.05_model.r INFO @ Tue, 16 Jun 2020 09:12:55: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:12:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:12:57: 18000000 INFO @ Tue, 16 Jun 2020 09:13:00: 16000000 INFO @ Tue, 16 Jun 2020 09:13:05: 19000000 INFO @ Tue, 16 Jun 2020 09:13:07: 17000000 INFO @ Tue, 16 Jun 2020 09:13:13: 20000000 INFO @ Tue, 16 Jun 2020 09:13:14: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:13:15: 18000000 INFO @ Tue, 16 Jun 2020 09:13:21: 21000000 INFO @ Tue, 16 Jun 2020 09:13:22: 19000000 INFO @ Tue, 16 Jun 2020 09:13:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085438/SRX4085438.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:13:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085438/SRX4085438.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:13:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085438/SRX4085438.05_summits.bed INFO @ Tue, 16 Jun 2020 09:13:23: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4493 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:13:29: 22000000 INFO @ Tue, 16 Jun 2020 09:13:29: 20000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:13:36: 21000000 INFO @ Tue, 16 Jun 2020 09:13:37: 23000000 INFO @ Tue, 16 Jun 2020 09:13:44: 22000000 INFO @ Tue, 16 Jun 2020 09:13:44: 24000000 INFO @ Tue, 16 Jun 2020 09:13:48: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:13:48: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:13:48: #1 total tags in treatment: 10452053 INFO @ Tue, 16 Jun 2020 09:13:48: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:13:48: #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 09:13:48: #1 tags after filtering in treatment: 8625845 INFO @ Tue, 16 Jun 2020 09:13:48: #1 Redundant rate of treatment: 0.17 INFO @ Tue, 16 Jun 2020 09:13:48: #1 finished! INFO @ Tue, 16 Jun 2020 09:13:48: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:13:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:13:48: #2 number of paired peaks: 533 WARNING @ Tue, 16 Jun 2020 09:13:48: Fewer paired peaks (533) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 533 pairs to build model! INFO @ Tue, 16 Jun 2020 09:13:48: start model_add_line... INFO @ Tue, 16 Jun 2020 09:13:48: start X-correlation... INFO @ Tue, 16 Jun 2020 09:13:48: end of X-cor INFO @ Tue, 16 Jun 2020 09:13:48: #2 finished! INFO @ Tue, 16 Jun 2020 09:13:48: #2 predicted fragment length is 107 bps INFO @ Tue, 16 Jun 2020 09:13:48: #2 alternative fragment length(s) may be 107 bps INFO @ Tue, 16 Jun 2020 09:13:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085438/SRX4085438.10_model.r INFO @ Tue, 16 Jun 2020 09:13:48: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:13:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:13:50: 23000000 INFO @ Tue, 16 Jun 2020 09:13:56: 24000000 INFO @ Tue, 16 Jun 2020 09:13:58: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:13:58: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:13:58: #1 total tags in treatment: 10452053 INFO @ Tue, 16 Jun 2020 09:13:58: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:13:58: #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 09:13:59: #1 tags after filtering in treatment: 8625845 INFO @ Tue, 16 Jun 2020 09:13:59: #1 Redundant rate of treatment: 0.17 INFO @ Tue, 16 Jun 2020 09:13:59: #1 finished! INFO @ Tue, 16 Jun 2020 09:13:59: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:13:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:13:59: #2 number of paired peaks: 533 WARNING @ Tue, 16 Jun 2020 09:13:59: Fewer paired peaks (533) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 533 pairs to build model! INFO @ Tue, 16 Jun 2020 09:13:59: start model_add_line... INFO @ Tue, 16 Jun 2020 09:13:59: start X-correlation... INFO @ Tue, 16 Jun 2020 09:13:59: end of X-cor INFO @ Tue, 16 Jun 2020 09:13:59: #2 finished! INFO @ Tue, 16 Jun 2020 09:13:59: #2 predicted fragment length is 107 bps INFO @ Tue, 16 Jun 2020 09:13:59: #2 alternative fragment length(s) may be 107 bps INFO @ Tue, 16 Jun 2020 09:13:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085438/SRX4085438.20_model.r INFO @ Tue, 16 Jun 2020 09:13:59: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:13:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:14:07: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:14:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085438/SRX4085438.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:14:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085438/SRX4085438.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:14:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085438/SRX4085438.10_summits.bed INFO @ Tue, 16 Jun 2020 09:14:16: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2853 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:14:18: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:14:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085438/SRX4085438.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:14:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085438/SRX4085438.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:14:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085438/SRX4085438.20_summits.bed INFO @ Tue, 16 Jun 2020 09:14:27: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1491 records, 4 fields): 3 millis CompletedMACS2peakCalling