Job ID = 6507799 SRX = SRX4085443 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-26T13:09:36 prefetch.2.10.7: 1) Downloading 'SRR7167472'... 2020-06-26T13:09:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:14:18 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:14:18 prefetch.2.10.7: 1) 'SRR7167472' was downloaded successfully Read 12951894 spots for SRR7167472/SRR7167472.sra Written 12951894 spots for SRR7167472/SRR7167472.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: 00:06:04 12951894 reads; of these: 12951894 (100.00%) were paired; of these: 8695371 (67.14%) aligned concordantly 0 times 3646020 (28.15%) aligned concordantly exactly 1 time 610503 (4.71%) aligned concordantly >1 times ---- 8695371 pairs aligned concordantly 0 times; of these: 180460 (2.08%) aligned discordantly 1 time ---- 8514911 pairs aligned 0 times concordantly or discordantly; of these: 17029822 mates make up the pairs; of these: 13775005 (80.89%) aligned 0 times 2778395 (16.31%) aligned exactly 1 time 476422 (2.80%) aligned >1 times 46.82% overall alignment rate Time searching: 00:06:04 Overall time: 00:06:04 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] 291253 / 4360971 = 0.0668 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 @ Fri, 26 Jun 2020 22:25:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085443/SRX4085443.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085443/SRX4085443.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085443/SRX4085443.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085443/SRX4085443.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 @ Fri, 26 Jun 2020 22:25:24: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:25:24: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:25:29: 1000000 INFO @ Fri, 26 Jun 2020 22:25:34: 2000000 INFO @ Fri, 26 Jun 2020 22:25:39: 3000000 INFO @ Fri, 26 Jun 2020 22:25:44: 4000000 INFO @ Fri, 26 Jun 2020 22:25:49: 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 @ Fri, 26 Jun 2020 22:25:54: 6000000 INFO @ Fri, 26 Jun 2020 22:25:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085443/SRX4085443.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085443/SRX4085443.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085443/SRX4085443.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085443/SRX4085443.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 @ Fri, 26 Jun 2020 22:25:54: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:25:54: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:25:59: 7000000 INFO @ Fri, 26 Jun 2020 22:26:00: 1000000 INFO @ Fri, 26 Jun 2020 22:26:04: 8000000 INFO @ Fri, 26 Jun 2020 22:26:06: 2000000 INFO @ Fri, 26 Jun 2020 22:26:09: 9000000 INFO @ Fri, 26 Jun 2020 22:26:12: 3000000 INFO @ Fri, 26 Jun 2020 22:26:14: 10000000 INFO @ Fri, 26 Jun 2020 22:26:17: 4000000 INFO @ Fri, 26 Jun 2020 22:26:19: 11000000 INFO @ Fri, 26 Jun 2020 22:26:22: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 22:26:22: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 22:26:22: #1 total tags in treatment: 3971871 INFO @ Fri, 26 Jun 2020 22:26:22: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:26:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:26:22: #1 tags after filtering in treatment: 3764238 INFO @ Fri, 26 Jun 2020 22:26:22: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 26 Jun 2020 22:26:22: #1 finished! INFO @ Fri, 26 Jun 2020 22:26:22: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:26:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:26:22: #2 number of paired peaks: 319 WARNING @ Fri, 26 Jun 2020 22:26:22: Fewer paired peaks (319) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 319 pairs to build model! INFO @ Fri, 26 Jun 2020 22:26:22: start model_add_line... INFO @ Fri, 26 Jun 2020 22:26:22: start X-correlation... INFO @ Fri, 26 Jun 2020 22:26:22: end of X-cor INFO @ Fri, 26 Jun 2020 22:26:22: #2 finished! INFO @ Fri, 26 Jun 2020 22:26:22: #2 predicted fragment length is 160 bps INFO @ Fri, 26 Jun 2020 22:26:22: #2 alternative fragment length(s) may be 92,160,173 bps INFO @ Fri, 26 Jun 2020 22:26:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085443/SRX4085443.05_model.r INFO @ Fri, 26 Jun 2020 22:26:22: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:26:22: #3 Pre-compute pvalue-qvalue table... 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 @ Fri, 26 Jun 2020 22:26:23: 5000000 INFO @ Fri, 26 Jun 2020 22:26:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085443/SRX4085443.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085443/SRX4085443.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085443/SRX4085443.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085443/SRX4085443.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 @ Fri, 26 Jun 2020 22:26:24: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:26:24: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:26:29: 6000000 INFO @ Fri, 26 Jun 2020 22:26:29: 1000000 INFO @ Fri, 26 Jun 2020 22:26:30: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:26:34: 2000000 INFO @ Fri, 26 Jun 2020 22:26:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085443/SRX4085443.05_peaks.xls INFO @ Fri, 26 Jun 2020 22:26:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085443/SRX4085443.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:26:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085443/SRX4085443.05_summits.bed INFO @ Fri, 26 Jun 2020 22:26:35: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (220 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:26:35: 7000000 INFO @ Fri, 26 Jun 2020 22:26:40: 3000000 INFO @ Fri, 26 Jun 2020 22:26:41: 8000000 INFO @ Fri, 26 Jun 2020 22:26:45: 4000000 INFO @ Fri, 26 Jun 2020 22:26:47: 9000000 INFO @ Fri, 26 Jun 2020 22:26:50: 5000000 INFO @ Fri, 26 Jun 2020 22:26:53: 10000000 INFO @ Fri, 26 Jun 2020 22:26:55: 6000000 INFO @ Fri, 26 Jun 2020 22:26:58: 11000000 INFO @ Fri, 26 Jun 2020 22:27:00: 7000000 INFO @ Fri, 26 Jun 2020 22:27:02: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 22:27:02: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 22:27:02: #1 total tags in treatment: 3971871 INFO @ Fri, 26 Jun 2020 22:27:02: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:27:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:27:02: #1 tags after filtering in treatment: 3764238 INFO @ Fri, 26 Jun 2020 22:27:02: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 26 Jun 2020 22:27:02: #1 finished! INFO @ Fri, 26 Jun 2020 22:27:02: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:27:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:27:02: #2 number of paired peaks: 319 WARNING @ Fri, 26 Jun 2020 22:27:02: Fewer paired peaks (319) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 319 pairs to build model! INFO @ Fri, 26 Jun 2020 22:27:02: start model_add_line... INFO @ Fri, 26 Jun 2020 22:27:02: start X-correlation... INFO @ Fri, 26 Jun 2020 22:27:02: end of X-cor INFO @ Fri, 26 Jun 2020 22:27:02: #2 finished! INFO @ Fri, 26 Jun 2020 22:27:02: #2 predicted fragment length is 160 bps INFO @ Fri, 26 Jun 2020 22:27:02: #2 alternative fragment length(s) may be 92,160,173 bps INFO @ Fri, 26 Jun 2020 22:27:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085443/SRX4085443.10_model.r INFO @ Fri, 26 Jun 2020 22:27:02: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:27:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:27:05: 8000000 INFO @ Fri, 26 Jun 2020 22:27:10: 9000000 INFO @ Fri, 26 Jun 2020 22:27:10: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:27:15: 10000000 INFO @ Fri, 26 Jun 2020 22:27:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085443/SRX4085443.10_peaks.xls INFO @ Fri, 26 Jun 2020 22:27:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085443/SRX4085443.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:27:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085443/SRX4085443.10_summits.bed INFO @ Fri, 26 Jun 2020 22:27:15: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (155 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:27:19: 11000000 INFO @ Fri, 26 Jun 2020 22:27:22: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 22:27:22: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 22:27:22: #1 total tags in treatment: 3971871 INFO @ Fri, 26 Jun 2020 22:27:22: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:27:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:27:22: #1 tags after filtering in treatment: 3764238 INFO @ Fri, 26 Jun 2020 22:27:22: #1 Redundant rate of treatment: 0.05 INFO @ Fri, 26 Jun 2020 22:27:22: #1 finished! INFO @ Fri, 26 Jun 2020 22:27:22: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:27:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:27:22: #2 number of paired peaks: 319 WARNING @ Fri, 26 Jun 2020 22:27:22: Fewer paired peaks (319) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 319 pairs to build model! INFO @ Fri, 26 Jun 2020 22:27:22: start model_add_line... INFO @ Fri, 26 Jun 2020 22:27:22: start X-correlation... INFO @ Fri, 26 Jun 2020 22:27:22: end of X-cor INFO @ Fri, 26 Jun 2020 22:27:22: #2 finished! INFO @ Fri, 26 Jun 2020 22:27:22: #2 predicted fragment length is 160 bps INFO @ Fri, 26 Jun 2020 22:27:22: #2 alternative fragment length(s) may be 92,160,173 bps INFO @ Fri, 26 Jun 2020 22:27:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085443/SRX4085443.20_model.r INFO @ Fri, 26 Jun 2020 22:27:22: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:27:22: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:27:31: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:27:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085443/SRX4085443.20_peaks.xls INFO @ Fri, 26 Jun 2020 22:27:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085443/SRX4085443.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:27:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085443/SRX4085443.20_summits.bed INFO @ Fri, 26 Jun 2020 22:27:35: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (87 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。