Job ID = 6367838 SRX = SRX4085406 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T23:39:59 prefetch.2.10.7: 1) Downloading 'SRR7167435'... 2020-06-15T23:39:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:53:23 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:53:24 prefetch.2.10.7: 1) 'SRR7167435' was downloaded successfully Read 41433735 spots for SRR7167435/SRR7167435.sra Written 41433735 spots for SRR7167435/SRR7167435.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: 00:32:36 41433735 reads; of these: 41433735 (100.00%) were paired; of these: 2697978 (6.51%) aligned concordantly 0 times 34258234 (82.68%) aligned concordantly exactly 1 time 4477523 (10.81%) aligned concordantly >1 times ---- 2697978 pairs aligned concordantly 0 times; of these: 636270 (23.58%) aligned discordantly 1 time ---- 2061708 pairs aligned 0 times concordantly or discordantly; of these: 4123416 mates make up the pairs; of these: 2417224 (58.62%) aligned 0 times 1340328 (32.51%) aligned exactly 1 time 365864 (8.87%) aligned >1 times 97.08% overall alignment rate Time searching: 00:32:36 Overall time: 00:32:36 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 36 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] 28147282 / 39111388 = 0.7197 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 09:46:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085406/SRX4085406.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085406/SRX4085406.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085406/SRX4085406.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085406/SRX4085406.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 09:46:11: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:46:11: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:46:17: 1000000 INFO @ Tue, 16 Jun 2020 09:46:23: 2000000 INFO @ Tue, 16 Jun 2020 09:46:29: 3000000 INFO @ Tue, 16 Jun 2020 09:46:35: 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 09:46:41: 5000000 INFO @ Tue, 16 Jun 2020 09:46:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085406/SRX4085406.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085406/SRX4085406.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085406/SRX4085406.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085406/SRX4085406.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 09:46:41: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:46:41: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:46:47: 6000000 INFO @ Tue, 16 Jun 2020 09:46:48: 1000000 INFO @ Tue, 16 Jun 2020 09:46:54: 7000000 INFO @ Tue, 16 Jun 2020 09:46:55: 2000000 INFO @ Tue, 16 Jun 2020 09:47:00: 8000000 INFO @ Tue, 16 Jun 2020 09:47:01: 3000000 INFO @ Tue, 16 Jun 2020 09:47:06: 9000000 INFO @ Tue, 16 Jun 2020 09:47:07: 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 09:47:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085406/SRX4085406.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085406/SRX4085406.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085406/SRX4085406.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085406/SRX4085406.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 09:47:11: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:47:11: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:47:12: 10000000 INFO @ Tue, 16 Jun 2020 09:47:14: 5000000 INFO @ Tue, 16 Jun 2020 09:47:18: 1000000 INFO @ Tue, 16 Jun 2020 09:47:18: 11000000 INFO @ Tue, 16 Jun 2020 09:47:21: 6000000 INFO @ Tue, 16 Jun 2020 09:47:24: 2000000 INFO @ Tue, 16 Jun 2020 09:47:25: 12000000 INFO @ Tue, 16 Jun 2020 09:47:27: 7000000 INFO @ Tue, 16 Jun 2020 09:47:31: 3000000 INFO @ Tue, 16 Jun 2020 09:47:31: 13000000 INFO @ Tue, 16 Jun 2020 09:47:34: 8000000 INFO @ Tue, 16 Jun 2020 09:47:37: 4000000 INFO @ Tue, 16 Jun 2020 09:47:37: 14000000 INFO @ Tue, 16 Jun 2020 09:47:40: 9000000 INFO @ Tue, 16 Jun 2020 09:47:43: 15000000 INFO @ Tue, 16 Jun 2020 09:47:43: 5000000 INFO @ Tue, 16 Jun 2020 09:47:47: 10000000 INFO @ Tue, 16 Jun 2020 09:47:49: 16000000 INFO @ Tue, 16 Jun 2020 09:47:50: 6000000 INFO @ Tue, 16 Jun 2020 09:47:54: 11000000 INFO @ Tue, 16 Jun 2020 09:47:56: 17000000 INFO @ Tue, 16 Jun 2020 09:47:56: 7000000 INFO @ Tue, 16 Jun 2020 09:48:00: 12000000 INFO @ Tue, 16 Jun 2020 09:48:02: 18000000 INFO @ Tue, 16 Jun 2020 09:48:02: 8000000 INFO @ Tue, 16 Jun 2020 09:48:07: 13000000 INFO @ Tue, 16 Jun 2020 09:48:08: 19000000 INFO @ Tue, 16 Jun 2020 09:48:09: 9000000 INFO @ Tue, 16 Jun 2020 09:48:14: 14000000 INFO @ Tue, 16 Jun 2020 09:48:14: 20000000 INFO @ Tue, 16 Jun 2020 09:48:15: 10000000 INFO @ Tue, 16 Jun 2020 09:48:20: 15000000 INFO @ Tue, 16 Jun 2020 09:48:20: 21000000 INFO @ Tue, 16 Jun 2020 09:48:21: 11000000 INFO @ Tue, 16 Jun 2020 09:48:27: 22000000 INFO @ Tue, 16 Jun 2020 09:48:27: 16000000 INFO @ Tue, 16 Jun 2020 09:48:28: 12000000 INFO @ Tue, 16 Jun 2020 09:48:34: 23000000 INFO @ Tue, 16 Jun 2020 09:48:34: 17000000 INFO @ Tue, 16 Jun 2020 09:48:34: 13000000 INFO @ Tue, 16 Jun 2020 09:48:40: 24000000 INFO @ Tue, 16 Jun 2020 09:48:40: 14000000 INFO @ Tue, 16 Jun 2020 09:48:40: 18000000 INFO @ Tue, 16 Jun 2020 09:48:41: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:48:41: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:48:41: #1 total tags in treatment: 10800689 INFO @ Tue, 16 Jun 2020 09:48:41: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:48:41: #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 09:48:41: #1 tags after filtering in treatment: 9498252 INFO @ Tue, 16 Jun 2020 09:48:41: #1 Redundant rate of treatment: 0.12 INFO @ Tue, 16 Jun 2020 09:48:41: #1 finished! INFO @ Tue, 16 Jun 2020 09:48:41: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:48:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:48:42: #2 number of paired peaks: 350 WARNING @ Tue, 16 Jun 2020 09:48:42: Fewer paired peaks (350) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 350 pairs to build model! INFO @ Tue, 16 Jun 2020 09:48:42: start model_add_line... INFO @ Tue, 16 Jun 2020 09:48:42: start X-correlation... INFO @ Tue, 16 Jun 2020 09:48:42: end of X-cor INFO @ Tue, 16 Jun 2020 09:48:42: #2 finished! INFO @ Tue, 16 Jun 2020 09:48:42: #2 predicted fragment length is 114 bps INFO @ Tue, 16 Jun 2020 09:48:42: #2 alternative fragment length(s) may be 3,89,91,114 bps INFO @ Tue, 16 Jun 2020 09:48:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085406/SRX4085406.05_model.r INFO @ Tue, 16 Jun 2020 09:48:42: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:48:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:48:47: 15000000 INFO @ Tue, 16 Jun 2020 09:48:47: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:48:53: 16000000 INFO @ Tue, 16 Jun 2020 09:48:54: 20000000 INFO @ Tue, 16 Jun 2020 09:48:59: 17000000 INFO @ Tue, 16 Jun 2020 09:49:00: 21000000 INFO @ Tue, 16 Jun 2020 09:49:02: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:49:06: 18000000 INFO @ Tue, 16 Jun 2020 09:49:07: 22000000 INFO @ Tue, 16 Jun 2020 09:49:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085406/SRX4085406.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:49:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085406/SRX4085406.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:49:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085406/SRX4085406.05_summits.bed INFO @ Tue, 16 Jun 2020 09:49:12: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (497 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:49:12: 19000000 INFO @ Tue, 16 Jun 2020 09:49:14: 23000000 INFO @ Tue, 16 Jun 2020 09:49:18: 20000000 INFO @ Tue, 16 Jun 2020 09:49:20: 24000000 INFO @ Tue, 16 Jun 2020 09:49:21: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:49:21: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:49:21: #1 total tags in treatment: 10800689 INFO @ Tue, 16 Jun 2020 09:49:21: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:49:21: #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 09:49:21: #1 tags after filtering in treatment: 9498252 INFO @ Tue, 16 Jun 2020 09:49:21: #1 Redundant rate of treatment: 0.12 INFO @ Tue, 16 Jun 2020 09:49:21: #1 finished! INFO @ Tue, 16 Jun 2020 09:49:21: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:49:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:49:22: #2 number of paired peaks: 350 WARNING @ Tue, 16 Jun 2020 09:49:22: Fewer paired peaks (350) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 350 pairs to build model! INFO @ Tue, 16 Jun 2020 09:49:22: start model_add_line... INFO @ Tue, 16 Jun 2020 09:49:22: start X-correlation... INFO @ Tue, 16 Jun 2020 09:49:22: end of X-cor INFO @ Tue, 16 Jun 2020 09:49:22: #2 finished! INFO @ Tue, 16 Jun 2020 09:49:22: #2 predicted fragment length is 114 bps INFO @ Tue, 16 Jun 2020 09:49:22: #2 alternative fragment length(s) may be 3,89,91,114 bps INFO @ Tue, 16 Jun 2020 09:49:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085406/SRX4085406.10_model.r INFO @ Tue, 16 Jun 2020 09:49:22: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:49:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:49:24: 21000000 INFO @ Tue, 16 Jun 2020 09:49:30: 22000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:49:36: 23000000 INFO @ Tue, 16 Jun 2020 09:49:42: 24000000 INFO @ Tue, 16 Jun 2020 09:49:43: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:49:43: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:49:43: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:49:43: #1 total tags in treatment: 10800689 INFO @ Tue, 16 Jun 2020 09:49:43: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:49:43: #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 09:49:44: #1 tags after filtering in treatment: 9498252 INFO @ Tue, 16 Jun 2020 09:49:44: #1 Redundant rate of treatment: 0.12 INFO @ Tue, 16 Jun 2020 09:49:44: #1 finished! INFO @ Tue, 16 Jun 2020 09:49:44: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:49:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:49:44: #2 number of paired peaks: 350 WARNING @ Tue, 16 Jun 2020 09:49:44: Fewer paired peaks (350) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 350 pairs to build model! INFO @ Tue, 16 Jun 2020 09:49:44: start model_add_line... INFO @ Tue, 16 Jun 2020 09:49:44: start X-correlation... INFO @ Tue, 16 Jun 2020 09:49:44: end of X-cor INFO @ Tue, 16 Jun 2020 09:49:44: #2 finished! INFO @ Tue, 16 Jun 2020 09:49:44: #2 predicted fragment length is 114 bps INFO @ Tue, 16 Jun 2020 09:49:44: #2 alternative fragment length(s) may be 3,89,91,114 bps INFO @ Tue, 16 Jun 2020 09:49:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085406/SRX4085406.20_model.r INFO @ Tue, 16 Jun 2020 09:49:44: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:49:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:49:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085406/SRX4085406.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:49:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085406/SRX4085406.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:49:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085406/SRX4085406.10_summits.bed INFO @ Tue, 16 Jun 2020 09:49:53: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (289 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:50:05: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:50:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085406/SRX4085406.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:50:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085406/SRX4085406.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:50:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085406/SRX4085406.20_summits.bed INFO @ Tue, 16 Jun 2020 09:50:15: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (169 records, 4 fields): 2 millis CompletedMACS2peakCalling