Job ID = 6367816 SRX = SRX4085384 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-16T00:01:15 prefetch.2.10.7: 1) Downloading 'SRR7167413'... 2020-06-16T00:01:15 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:04:21 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:04:21 prefetch.2.10.7: 1) 'SRR7167413' was downloaded successfully Read 17580922 spots for SRR7167413/SRR7167413.sra Written 17580922 spots for SRR7167413/SRR7167413.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: 00:11:23 17580922 reads; of these: 17580922 (100.00%) were paired; of these: 9574145 (54.46%) aligned concordantly 0 times 6822244 (38.80%) aligned concordantly exactly 1 time 1184533 (6.74%) aligned concordantly >1 times ---- 9574145 pairs aligned concordantly 0 times; of these: 265300 (2.77%) aligned discordantly 1 time ---- 9308845 pairs aligned 0 times concordantly or discordantly; of these: 18617690 mates make up the pairs; of these: 13629552 (73.21%) aligned 0 times 4358125 (23.41%) aligned exactly 1 time 630013 (3.38%) aligned >1 times 61.24% overall alignment rate Time searching: 00:11:23 Overall time: 00:11:23 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] 1892128 / 8149928 = 0.2322 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 09:23:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085384/SRX4085384.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085384/SRX4085384.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085384/SRX4085384.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085384/SRX4085384.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 09:23:47: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:23:47: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:23:54: 1000000 INFO @ Tue, 16 Jun 2020 09:24:00: 2000000 INFO @ Tue, 16 Jun 2020 09:24:05: 3000000 INFO @ Tue, 16 Jun 2020 09:24:11: 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 09:24:16: 5000000 INFO @ Tue, 16 Jun 2020 09:24:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085384/SRX4085384.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085384/SRX4085384.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085384/SRX4085384.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085384/SRX4085384.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 09:24:17: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:24:17: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:24:22: 6000000 INFO @ Tue, 16 Jun 2020 09:24:24: 1000000 INFO @ Tue, 16 Jun 2020 09:24:28: 7000000 INFO @ Tue, 16 Jun 2020 09:24:30: 2000000 INFO @ Tue, 16 Jun 2020 09:24:35: 8000000 INFO @ Tue, 16 Jun 2020 09:24:36: 3000000 INFO @ Tue, 16 Jun 2020 09:24:41: 9000000 INFO @ Tue, 16 Jun 2020 09:24:42: 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 09:24:47: 10000000 INFO @ Tue, 16 Jun 2020 09:24:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085384/SRX4085384.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085384/SRX4085384.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085384/SRX4085384.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085384/SRX4085384.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 09:24:47: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:24:47: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:24:48: 5000000 INFO @ Tue, 16 Jun 2020 09:24:53: 11000000 INFO @ Tue, 16 Jun 2020 09:24:54: 1000000 INFO @ Tue, 16 Jun 2020 09:24:55: 6000000 INFO @ Tue, 16 Jun 2020 09:24:59: 12000000 INFO @ Tue, 16 Jun 2020 09:25:00: 2000000 INFO @ Tue, 16 Jun 2020 09:25:01: 7000000 INFO @ Tue, 16 Jun 2020 09:25:05: 13000000 INFO @ Tue, 16 Jun 2020 09:25:06: 3000000 INFO @ Tue, 16 Jun 2020 09:25:07: 8000000 INFO @ Tue, 16 Jun 2020 09:25:12: 14000000 INFO @ Tue, 16 Jun 2020 09:25:12: 4000000 INFO @ Tue, 16 Jun 2020 09:25:14: 9000000 INFO @ Tue, 16 Jun 2020 09:25:18: 15000000 INFO @ Tue, 16 Jun 2020 09:25:19: 5000000 INFO @ Tue, 16 Jun 2020 09:25:20: 10000000 INFO @ Tue, 16 Jun 2020 09:25:24: 16000000 INFO @ Tue, 16 Jun 2020 09:25:25: 6000000 INFO @ Tue, 16 Jun 2020 09:25:27: 11000000 INFO @ Tue, 16 Jun 2020 09:25:30: 17000000 INFO @ Tue, 16 Jun 2020 09:25:31: 7000000 INFO @ Tue, 16 Jun 2020 09:25:33: 12000000 INFO @ Tue, 16 Jun 2020 09:25:34: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:25:34: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:25:34: #1 total tags in treatment: 6145717 INFO @ Tue, 16 Jun 2020 09:25:34: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:25:34: #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 09:25:34: #1 tags after filtering in treatment: 5530302 INFO @ Tue, 16 Jun 2020 09:25:34: #1 Redundant rate of treatment: 0.10 INFO @ Tue, 16 Jun 2020 09:25:34: #1 finished! INFO @ Tue, 16 Jun 2020 09:25:34: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:25:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:25:35: #2 number of paired peaks: 394 WARNING @ Tue, 16 Jun 2020 09:25:35: Fewer paired peaks (394) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 394 pairs to build model! INFO @ Tue, 16 Jun 2020 09:25:35: start model_add_line... INFO @ Tue, 16 Jun 2020 09:25:35: start X-correlation... INFO @ Tue, 16 Jun 2020 09:25:35: end of X-cor INFO @ Tue, 16 Jun 2020 09:25:35: #2 finished! INFO @ Tue, 16 Jun 2020 09:25:35: #2 predicted fragment length is 105 bps INFO @ Tue, 16 Jun 2020 09:25:35: #2 alternative fragment length(s) may be 4,105,124 bps INFO @ Tue, 16 Jun 2020 09:25:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085384/SRX4085384.05_model.r INFO @ Tue, 16 Jun 2020 09:25:35: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:25:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:25:37: 8000000 INFO @ Tue, 16 Jun 2020 09:25:39: 13000000 INFO @ Tue, 16 Jun 2020 09:25:43: 9000000 INFO @ Tue, 16 Jun 2020 09:25:45: 14000000 INFO @ Tue, 16 Jun 2020 09:25:48: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:25:50: 10000000 INFO @ Tue, 16 Jun 2020 09:25:51: 15000000 INFO @ Tue, 16 Jun 2020 09:25:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085384/SRX4085384.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:25:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085384/SRX4085384.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:25:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085384/SRX4085384.05_summits.bed INFO @ Tue, 16 Jun 2020 09:25:54: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (981 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:25:56: 11000000 INFO @ Tue, 16 Jun 2020 09:25:58: 16000000 INFO @ Tue, 16 Jun 2020 09:26:02: 12000000 INFO @ Tue, 16 Jun 2020 09:26:04: 17000000 INFO @ Tue, 16 Jun 2020 09:26:08: 13000000 INFO @ Tue, 16 Jun 2020 09:26:08: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:26:08: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:26:08: #1 total tags in treatment: 6145717 INFO @ Tue, 16 Jun 2020 09:26:08: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:26:08: #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 09:26:08: #1 tags after filtering in treatment: 5530302 INFO @ Tue, 16 Jun 2020 09:26:08: #1 Redundant rate of treatment: 0.10 INFO @ Tue, 16 Jun 2020 09:26:08: #1 finished! INFO @ Tue, 16 Jun 2020 09:26:08: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:26:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:26:08: #2 number of paired peaks: 394 WARNING @ Tue, 16 Jun 2020 09:26:08: Fewer paired peaks (394) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 394 pairs to build model! INFO @ Tue, 16 Jun 2020 09:26:08: start model_add_line... INFO @ Tue, 16 Jun 2020 09:26:09: start X-correlation... INFO @ Tue, 16 Jun 2020 09:26:09: end of X-cor INFO @ Tue, 16 Jun 2020 09:26:09: #2 finished! INFO @ Tue, 16 Jun 2020 09:26:09: #2 predicted fragment length is 105 bps INFO @ Tue, 16 Jun 2020 09:26:09: #2 alternative fragment length(s) may be 4,105,124 bps INFO @ Tue, 16 Jun 2020 09:26:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085384/SRX4085384.10_model.r INFO @ Tue, 16 Jun 2020 09:26:09: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:26:09: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:26:13: 14000000 INFO @ Tue, 16 Jun 2020 09:26:19: 15000000 INFO @ Tue, 16 Jun 2020 09:26:21: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:26:24: 16000000 INFO @ Tue, 16 Jun 2020 09:26:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085384/SRX4085384.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:26:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085384/SRX4085384.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:26:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085384/SRX4085384.10_summits.bed INFO @ Tue, 16 Jun 2020 09:26:27: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (498 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:26:30: 17000000 INFO @ Tue, 16 Jun 2020 09:26:34: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:26:34: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:26:34: #1 total tags in treatment: 6145717 INFO @ Tue, 16 Jun 2020 09:26:34: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:26:34: #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 09:26:34: #1 tags after filtering in treatment: 5530302 INFO @ Tue, 16 Jun 2020 09:26:34: #1 Redundant rate of treatment: 0.10 INFO @ Tue, 16 Jun 2020 09:26:34: #1 finished! INFO @ Tue, 16 Jun 2020 09:26:34: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:26:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:26:34: #2 number of paired peaks: 394 WARNING @ Tue, 16 Jun 2020 09:26:34: Fewer paired peaks (394) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 394 pairs to build model! INFO @ Tue, 16 Jun 2020 09:26:34: start model_add_line... INFO @ Tue, 16 Jun 2020 09:26:35: start X-correlation... INFO @ Tue, 16 Jun 2020 09:26:35: end of X-cor INFO @ Tue, 16 Jun 2020 09:26:35: #2 finished! INFO @ Tue, 16 Jun 2020 09:26:35: #2 predicted fragment length is 105 bps INFO @ Tue, 16 Jun 2020 09:26:35: #2 alternative fragment length(s) may be 4,105,124 bps INFO @ Tue, 16 Jun 2020 09:26:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085384/SRX4085384.20_model.r INFO @ Tue, 16 Jun 2020 09:26:35: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:26:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:26:47: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:26:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085384/SRX4085384.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:26:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085384/SRX4085384.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:26:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085384/SRX4085384.20_summits.bed INFO @ Tue, 16 Jun 2020 09:26:53: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (212 records, 4 fields): 1 millis CompletedMACS2peakCalling