Job ID = 6367819 SRX = SRX4085387 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T23:43:44 prefetch.2.10.7: 1) Downloading 'SRR7167416'... 2020-06-15T23:43:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:49:47 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:49:47 prefetch.2.10.7: 1) 'SRR7167416' was downloaded successfully Read 16752074 spots for SRR7167416/SRR7167416.sra Written 16752074 spots for SRR7167416/SRR7167416.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: 00:10:54 16752074 reads; of these: 16752074 (100.00%) were paired; of these: 6044979 (36.08%) aligned concordantly 0 times 9236451 (55.14%) aligned concordantly exactly 1 time 1470644 (8.78%) aligned concordantly >1 times ---- 6044979 pairs aligned concordantly 0 times; of these: 366584 (6.06%) aligned discordantly 1 time ---- 5678395 pairs aligned 0 times concordantly or discordantly; of these: 11356790 mates make up the pairs; of these: 7900510 (69.57%) aligned 0 times 3008243 (26.49%) aligned exactly 1 time 448037 (3.95%) aligned >1 times 76.42% overall alignment rate Time searching: 00:10:54 Overall time: 00:10:54 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] 734759 / 10914774 = 0.0673 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 09:09:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085387/SRX4085387.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085387/SRX4085387.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085387/SRX4085387.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085387/SRX4085387.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 09:09:22: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:09:22: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:09:27: 1000000 INFO @ Tue, 16 Jun 2020 09:09:32: 2000000 INFO @ Tue, 16 Jun 2020 09:09:36: 3000000 INFO @ Tue, 16 Jun 2020 09:09:40: 4000000 INFO @ Tue, 16 Jun 2020 09:09:45: 5000000 INFO @ Tue, 16 Jun 2020 09:09:49: 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 09:09:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085387/SRX4085387.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085387/SRX4085387.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085387/SRX4085387.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085387/SRX4085387.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 09:09:52: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:09:52: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:09:54: 7000000 INFO @ Tue, 16 Jun 2020 09:09:57: 1000000 INFO @ Tue, 16 Jun 2020 09:09:58: 8000000 INFO @ Tue, 16 Jun 2020 09:10:02: 2000000 INFO @ Tue, 16 Jun 2020 09:10:03: 9000000 INFO @ Tue, 16 Jun 2020 09:10:08: 3000000 INFO @ Tue, 16 Jun 2020 09:10:08: 10000000 INFO @ Tue, 16 Jun 2020 09:10:12: 11000000 INFO @ Tue, 16 Jun 2020 09:10:13: 4000000 INFO @ Tue, 16 Jun 2020 09:10:17: 12000000 INFO @ Tue, 16 Jun 2020 09:10:18: 5000000 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 09:10:22: 13000000 INFO @ Tue, 16 Jun 2020 09:10:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085387/SRX4085387.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085387/SRX4085387.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085387/SRX4085387.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085387/SRX4085387.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 09:10:23: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:10:23: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:10:23: 6000000 INFO @ Tue, 16 Jun 2020 09:10:27: 14000000 INFO @ Tue, 16 Jun 2020 09:10:27: 1000000 INFO @ Tue, 16 Jun 2020 09:10:28: 7000000 INFO @ Tue, 16 Jun 2020 09:10:32: 15000000 INFO @ Tue, 16 Jun 2020 09:10:33: 2000000 INFO @ Tue, 16 Jun 2020 09:10:33: 8000000 INFO @ Tue, 16 Jun 2020 09:10:37: 16000000 INFO @ Tue, 16 Jun 2020 09:10:37: 9000000 INFO @ Tue, 16 Jun 2020 09:10:38: 3000000 INFO @ Tue, 16 Jun 2020 09:10:41: 17000000 INFO @ Tue, 16 Jun 2020 09:10:42: 10000000 INFO @ Tue, 16 Jun 2020 09:10:43: 4000000 INFO @ Tue, 16 Jun 2020 09:10:46: 18000000 INFO @ Tue, 16 Jun 2020 09:10:47: 11000000 INFO @ Tue, 16 Jun 2020 09:10:49: 5000000 INFO @ Tue, 16 Jun 2020 09:10:51: 19000000 INFO @ Tue, 16 Jun 2020 09:10:51: 12000000 INFO @ Tue, 16 Jun 2020 09:10:53: 6000000 INFO @ Tue, 16 Jun 2020 09:10:56: 20000000 INFO @ Tue, 16 Jun 2020 09:10:57: 13000000 INFO @ Tue, 16 Jun 2020 09:10:58: 7000000 INFO @ Tue, 16 Jun 2020 09:11:00: 21000000 INFO @ Tue, 16 Jun 2020 09:11:02: 14000000 INFO @ Tue, 16 Jun 2020 09:11:03: 8000000 INFO @ Tue, 16 Jun 2020 09:11:05: 22000000 INFO @ Tue, 16 Jun 2020 09:11:08: 9000000 INFO @ Tue, 16 Jun 2020 09:11:08: 15000000 INFO @ Tue, 16 Jun 2020 09:11:10: 23000000 INFO @ Tue, 16 Jun 2020 09:11:13: 10000000 INFO @ Tue, 16 Jun 2020 09:11:14: 16000000 INFO @ Tue, 16 Jun 2020 09:11:14: 24000000 INFO @ Tue, 16 Jun 2020 09:11:15: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:11:15: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:11:15: #1 total tags in treatment: 9985190 INFO @ Tue, 16 Jun 2020 09:11:15: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:11:15: #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 09:11:15: #1 tags after filtering in treatment: 8755007 INFO @ Tue, 16 Jun 2020 09:11:15: #1 Redundant rate of treatment: 0.12 INFO @ Tue, 16 Jun 2020 09:11:15: #1 finished! INFO @ Tue, 16 Jun 2020 09:11:15: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:11:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:11:16: #2 number of paired peaks: 267 WARNING @ Tue, 16 Jun 2020 09:11:16: Fewer paired peaks (267) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 267 pairs to build model! INFO @ Tue, 16 Jun 2020 09:11:16: start model_add_line... INFO @ Tue, 16 Jun 2020 09:11:16: start X-correlation... INFO @ Tue, 16 Jun 2020 09:11:16: end of X-cor INFO @ Tue, 16 Jun 2020 09:11:16: #2 finished! INFO @ Tue, 16 Jun 2020 09:11:16: #2 predicted fragment length is 103 bps INFO @ Tue, 16 Jun 2020 09:11:16: #2 alternative fragment length(s) may be 4,103 bps INFO @ Tue, 16 Jun 2020 09:11:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085387/SRX4085387.05_model.r INFO @ Tue, 16 Jun 2020 09:11:16: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:11:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:11:18: 11000000 INFO @ Tue, 16 Jun 2020 09:11:19: 17000000 INFO @ Tue, 16 Jun 2020 09:11:22: 12000000 INFO @ Tue, 16 Jun 2020 09:11:25: 18000000 INFO @ Tue, 16 Jun 2020 09:11:28: 13000000 INFO @ Tue, 16 Jun 2020 09:11:30: 19000000 INFO @ Tue, 16 Jun 2020 09:11:33: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:11:33: 14000000 INFO @ Tue, 16 Jun 2020 09:11:36: 20000000 INFO @ Tue, 16 Jun 2020 09:11:39: 15000000 INFO @ Tue, 16 Jun 2020 09:11:41: 21000000 INFO @ Tue, 16 Jun 2020 09:11:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085387/SRX4085387.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:11:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085387/SRX4085387.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:11:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085387/SRX4085387.05_summits.bed INFO @ Tue, 16 Jun 2020 09:11:42: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (2295 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:11:45: 16000000 INFO @ Tue, 16 Jun 2020 09:11:47: 22000000 INFO @ Tue, 16 Jun 2020 09:11:51: 17000000 INFO @ Tue, 16 Jun 2020 09:11:52: 23000000 INFO @ Tue, 16 Jun 2020 09:11:56: 18000000 INFO @ Tue, 16 Jun 2020 09:11:58: 24000000 INFO @ Tue, 16 Jun 2020 09:11:59: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:11:59: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:11:59: #1 total tags in treatment: 9985190 INFO @ Tue, 16 Jun 2020 09:11:59: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:11:59: #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 09:11:59: #1 tags after filtering in treatment: 8755007 INFO @ Tue, 16 Jun 2020 09:11:59: #1 Redundant rate of treatment: 0.12 INFO @ Tue, 16 Jun 2020 09:11:59: #1 finished! INFO @ Tue, 16 Jun 2020 09:11:59: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:11:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:11:59: #2 number of paired peaks: 267 WARNING @ Tue, 16 Jun 2020 09:11:59: Fewer paired peaks (267) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 267 pairs to build model! INFO @ Tue, 16 Jun 2020 09:11:59: start model_add_line... INFO @ Tue, 16 Jun 2020 09:11:59: start X-correlation... INFO @ Tue, 16 Jun 2020 09:11:59: end of X-cor INFO @ Tue, 16 Jun 2020 09:11:59: #2 finished! INFO @ Tue, 16 Jun 2020 09:11:59: #2 predicted fragment length is 103 bps INFO @ Tue, 16 Jun 2020 09:11:59: #2 alternative fragment length(s) may be 4,103 bps INFO @ Tue, 16 Jun 2020 09:11:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085387/SRX4085387.10_model.r INFO @ Tue, 16 Jun 2020 09:11:59: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:11:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:12:02: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:12:08: 20000000 INFO @ Tue, 16 Jun 2020 09:12:13: 21000000 INFO @ Tue, 16 Jun 2020 09:12:18: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:12:19: 22000000 INFO @ Tue, 16 Jun 2020 09:12:24: 23000000 INFO @ Tue, 16 Jun 2020 09:12:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085387/SRX4085387.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:12:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085387/SRX4085387.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:12:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085387/SRX4085387.10_summits.bed INFO @ Tue, 16 Jun 2020 09:12:27: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1156 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:12:30: 24000000 INFO @ Tue, 16 Jun 2020 09:12:31: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:12:31: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:12:31: #1 total tags in treatment: 9985190 INFO @ Tue, 16 Jun 2020 09:12:31: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:12:31: #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 09:12:31: #1 tags after filtering in treatment: 8755007 INFO @ Tue, 16 Jun 2020 09:12:31: #1 Redundant rate of treatment: 0.12 INFO @ Tue, 16 Jun 2020 09:12:31: #1 finished! INFO @ Tue, 16 Jun 2020 09:12:31: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:12:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:12:32: #2 number of paired peaks: 267 WARNING @ Tue, 16 Jun 2020 09:12:32: Fewer paired peaks (267) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 267 pairs to build model! INFO @ Tue, 16 Jun 2020 09:12:32: start model_add_line... INFO @ Tue, 16 Jun 2020 09:12:32: start X-correlation... INFO @ Tue, 16 Jun 2020 09:12:32: end of X-cor INFO @ Tue, 16 Jun 2020 09:12:32: #2 finished! INFO @ Tue, 16 Jun 2020 09:12:32: #2 predicted fragment length is 103 bps INFO @ Tue, 16 Jun 2020 09:12:32: #2 alternative fragment length(s) may be 4,103 bps INFO @ Tue, 16 Jun 2020 09:12:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085387/SRX4085387.20_model.r INFO @ Tue, 16 Jun 2020 09:12:32: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:12:32: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:12:51: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:13:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085387/SRX4085387.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:13:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085387/SRX4085387.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:13:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085387/SRX4085387.20_summits.bed INFO @ Tue, 16 Jun 2020 09:13:00: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (362 records, 4 fields): 2 millis CompletedMACS2peakCalling