Job ID = 6367874 SRX = SRX4085441 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T23:40:44 prefetch.2.10.7: 1) Downloading 'SRR7167470'... 2020-06-15T23:40:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:46:56 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:46:56 prefetch.2.10.7: 1) 'SRR7167470' was downloaded successfully Read 14155206 spots for SRR7167470/SRR7167470.sra Written 14155206 spots for SRR7167470/SRR7167470.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: 00:07:27 14155206 reads; of these: 14155206 (100.00%) were paired; of these: 8227831 (58.13%) aligned concordantly 0 times 5084859 (35.92%) aligned concordantly exactly 1 time 842516 (5.95%) aligned concordantly >1 times ---- 8227831 pairs aligned concordantly 0 times; of these: 150807 (1.83%) aligned discordantly 1 time ---- 8077024 pairs aligned 0 times concordantly or discordantly; of these: 16154048 mates make up the pairs; of these: 12353796 (76.47%) aligned 0 times 3365382 (20.83%) aligned exactly 1 time 434870 (2.69%) aligned >1 times 56.36% overall alignment rate Time searching: 00:07:27 Overall time: 00:07:27 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 8 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] 537201 / 6012936 = 0.0893 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 09:00:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085441/SRX4085441.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085441/SRX4085441.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085441/SRX4085441.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085441/SRX4085441.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 09:00:30: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:00:30: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:00:35: 1000000 INFO @ Tue, 16 Jun 2020 09:00:39: 2000000 INFO @ Tue, 16 Jun 2020 09:00:44: 3000000 INFO @ Tue, 16 Jun 2020 09:00:49: 4000000 INFO @ Tue, 16 Jun 2020 09:00:54: 5000000 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 09:00:58: 6000000 INFO @ Tue, 16 Jun 2020 09:01:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085441/SRX4085441.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085441/SRX4085441.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085441/SRX4085441.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085441/SRX4085441.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 09:01:00: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:01:00: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:01:03: 7000000 INFO @ Tue, 16 Jun 2020 09:01:06: 1000000 INFO @ Tue, 16 Jun 2020 09:01:08: 8000000 INFO @ Tue, 16 Jun 2020 09:01:12: 2000000 INFO @ Tue, 16 Jun 2020 09:01:13: 9000000 INFO @ Tue, 16 Jun 2020 09:01:18: 3000000 INFO @ Tue, 16 Jun 2020 09:01:19: 10000000 INFO @ Tue, 16 Jun 2020 09:01:24: 11000000 INFO @ Tue, 16 Jun 2020 09:01:24: 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 09:01:29: 12000000 INFO @ Tue, 16 Jun 2020 09:01:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085441/SRX4085441.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085441/SRX4085441.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085441/SRX4085441.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085441/SRX4085441.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 09:01:30: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:01:30: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:01:30: 5000000 INFO @ Tue, 16 Jun 2020 09:01:34: 13000000 INFO @ Tue, 16 Jun 2020 09:01:35: 1000000 INFO @ Tue, 16 Jun 2020 09:01:37: 6000000 INFO @ Tue, 16 Jun 2020 09:01:39: 14000000 INFO @ Tue, 16 Jun 2020 09:01:40: 2000000 INFO @ Tue, 16 Jun 2020 09:01:43: 7000000 INFO @ Tue, 16 Jun 2020 09:01:44: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:01:44: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:01:44: #1 total tags in treatment: 5395572 INFO @ Tue, 16 Jun 2020 09:01:44: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:01:44: #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 09:01:44: #1 tags after filtering in treatment: 4898191 INFO @ Tue, 16 Jun 2020 09:01:44: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 16 Jun 2020 09:01:44: #1 finished! INFO @ Tue, 16 Jun 2020 09:01:44: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:01:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:01:44: #2 number of paired peaks: 259 WARNING @ Tue, 16 Jun 2020 09:01:44: Fewer paired peaks (259) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 259 pairs to build model! INFO @ Tue, 16 Jun 2020 09:01:44: start model_add_line... INFO @ Tue, 16 Jun 2020 09:01:44: start X-correlation... INFO @ Tue, 16 Jun 2020 09:01:44: end of X-cor INFO @ Tue, 16 Jun 2020 09:01:44: #2 finished! INFO @ Tue, 16 Jun 2020 09:01:44: #2 predicted fragment length is 104 bps INFO @ Tue, 16 Jun 2020 09:01:44: #2 alternative fragment length(s) may be 104 bps INFO @ Tue, 16 Jun 2020 09:01:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085441/SRX4085441.05_model.r INFO @ Tue, 16 Jun 2020 09:01:44: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:01:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:01:46: 3000000 INFO @ Tue, 16 Jun 2020 09:01:49: 8000000 INFO @ Tue, 16 Jun 2020 09:01:51: 4000000 INFO @ Tue, 16 Jun 2020 09:01:55: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:01:55: 9000000 INFO @ Tue, 16 Jun 2020 09:01:56: 5000000 INFO @ Tue, 16 Jun 2020 09:02:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085441/SRX4085441.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:02:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085441/SRX4085441.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:02:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085441/SRX4085441.05_summits.bed INFO @ Tue, 16 Jun 2020 09:02:00: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1209 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:02:01: 6000000 INFO @ Tue, 16 Jun 2020 09:02:01: 10000000 INFO @ Tue, 16 Jun 2020 09:02:07: 7000000 INFO @ Tue, 16 Jun 2020 09:02:08: 11000000 INFO @ Tue, 16 Jun 2020 09:02:12: 8000000 INFO @ Tue, 16 Jun 2020 09:02:14: 12000000 INFO @ Tue, 16 Jun 2020 09:02:17: 9000000 INFO @ Tue, 16 Jun 2020 09:02:20: 13000000 INFO @ Tue, 16 Jun 2020 09:02:22: 10000000 INFO @ Tue, 16 Jun 2020 09:02:26: 14000000 INFO @ Tue, 16 Jun 2020 09:02:27: 11000000 INFO @ Tue, 16 Jun 2020 09:02:31: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:02:31: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:02:31: #1 total tags in treatment: 5395572 INFO @ Tue, 16 Jun 2020 09:02:31: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:02:31: #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 09:02:31: #1 tags after filtering in treatment: 4898191 INFO @ Tue, 16 Jun 2020 09:02:31: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 16 Jun 2020 09:02:31: #1 finished! INFO @ Tue, 16 Jun 2020 09:02:31: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:02:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:02:32: #2 number of paired peaks: 259 WARNING @ Tue, 16 Jun 2020 09:02:32: Fewer paired peaks (259) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 259 pairs to build model! INFO @ Tue, 16 Jun 2020 09:02:32: start model_add_line... INFO @ Tue, 16 Jun 2020 09:02:32: start X-correlation... INFO @ Tue, 16 Jun 2020 09:02:32: end of X-cor INFO @ Tue, 16 Jun 2020 09:02:32: #2 finished! INFO @ Tue, 16 Jun 2020 09:02:32: #2 predicted fragment length is 104 bps INFO @ Tue, 16 Jun 2020 09:02:32: #2 alternative fragment length(s) may be 104 bps INFO @ Tue, 16 Jun 2020 09:02:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085441/SRX4085441.10_model.r INFO @ Tue, 16 Jun 2020 09:02:32: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:02:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:02:33: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:02:38: 13000000 INFO @ Tue, 16 Jun 2020 09:02:42: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:02:43: 14000000 INFO @ Tue, 16 Jun 2020 09:02:47: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:02:47: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:02:47: #1 total tags in treatment: 5395572 INFO @ Tue, 16 Jun 2020 09:02:47: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:02:47: #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 09:02:47: #1 tags after filtering in treatment: 4898191 INFO @ Tue, 16 Jun 2020 09:02:47: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 16 Jun 2020 09:02:47: #1 finished! INFO @ Tue, 16 Jun 2020 09:02:47: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:02:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:02:48: #2 number of paired peaks: 259 WARNING @ Tue, 16 Jun 2020 09:02:48: Fewer paired peaks (259) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 259 pairs to build model! INFO @ Tue, 16 Jun 2020 09:02:48: start model_add_line... INFO @ Tue, 16 Jun 2020 09:02:48: start X-correlation... INFO @ Tue, 16 Jun 2020 09:02:48: end of X-cor INFO @ Tue, 16 Jun 2020 09:02:48: #2 finished! INFO @ Tue, 16 Jun 2020 09:02:48: #2 predicted fragment length is 104 bps INFO @ Tue, 16 Jun 2020 09:02:48: #2 alternative fragment length(s) may be 104 bps INFO @ Tue, 16 Jun 2020 09:02:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085441/SRX4085441.20_model.r INFO @ Tue, 16 Jun 2020 09:02:48: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:02:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:02:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085441/SRX4085441.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:02:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085441/SRX4085441.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:02:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085441/SRX4085441.10_summits.bed INFO @ Tue, 16 Jun 2020 09:02:48: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (427 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:02:58: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:03:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085441/SRX4085441.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:03:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085441/SRX4085441.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:03:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085441/SRX4085441.20_summits.bed INFO @ Tue, 16 Jun 2020 09:03:03: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (111 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。