Job ID = 14519611 SRX = SRX6581723 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 22812529 spots for SRR9825056/SRR9825056.sra Written 22812529 spots for SRR9825056/SRR9825056.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: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:31:29 22812529 reads; of these: 22812529 (100.00%) were unpaired; of these: 662649 (2.90%) aligned 0 times 16529536 (72.46%) aligned exactly 1 time 5620344 (24.64%) aligned >1 times 97.10% overall alignment rate Time searching: 00:31:34 Overall time: 00:31:34 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 7236832 / 22149880 = 0.3267 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 17:22:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX6581723/SRX6581723.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX6581723/SRX6581723.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX6581723/SRX6581723.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX6581723/SRX6581723.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 15 Jan 2022 17:22:29: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:22:29: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:22:36: 1000000 INFO @ Sat, 15 Jan 2022 17:22:44: 2000000 INFO @ Sat, 15 Jan 2022 17:22:51: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 17:22:58: 4000000 INFO @ Sat, 15 Jan 2022 17:22:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX6581723/SRX6581723.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX6581723/SRX6581723.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX6581723/SRX6581723.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX6581723/SRX6581723.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 15 Jan 2022 17:22:58: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:22:58: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:23:06: 5000000 INFO @ Sat, 15 Jan 2022 17:23:06: 1000000 INFO @ Sat, 15 Jan 2022 17:23:14: 6000000 INFO @ Sat, 15 Jan 2022 17:23:14: 2000000 INFO @ Sat, 15 Jan 2022 17:23:22: 7000000 INFO @ Sat, 15 Jan 2022 17:23:22: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 17:23:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX6581723/SRX6581723.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX6581723/SRX6581723.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX6581723/SRX6581723.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX6581723/SRX6581723.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 15 Jan 2022 17:23:28: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:23:28: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:23:30: 8000000 INFO @ Sat, 15 Jan 2022 17:23:30: 4000000 INFO @ Sat, 15 Jan 2022 17:23:37: 1000000 INFO @ Sat, 15 Jan 2022 17:23:38: 9000000 INFO @ Sat, 15 Jan 2022 17:23:39: 5000000 INFO @ Sat, 15 Jan 2022 17:23:46: 2000000 INFO @ Sat, 15 Jan 2022 17:23:47: 10000000 INFO @ Sat, 15 Jan 2022 17:23:47: 6000000 INFO @ Sat, 15 Jan 2022 17:23:55: 11000000 INFO @ Sat, 15 Jan 2022 17:23:55: 3000000 INFO @ Sat, 15 Jan 2022 17:23:56: 7000000 INFO @ Sat, 15 Jan 2022 17:24:04: 12000000 INFO @ Sat, 15 Jan 2022 17:24:04: 4000000 INFO @ Sat, 15 Jan 2022 17:24:04: 8000000 INFO @ Sat, 15 Jan 2022 17:24:12: 13000000 INFO @ Sat, 15 Jan 2022 17:24:13: 9000000 INFO @ Sat, 15 Jan 2022 17:24:13: 5000000 INFO @ Sat, 15 Jan 2022 17:24:20: 14000000 INFO @ Sat, 15 Jan 2022 17:24:21: 10000000 INFO @ Sat, 15 Jan 2022 17:24:22: 6000000 INFO @ Sat, 15 Jan 2022 17:24:29: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 17:24:29: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 17:24:29: #1 total tags in treatment: 14913048 INFO @ Sat, 15 Jan 2022 17:24:29: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:24:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 17:24:29: #1 tags after filtering in treatment: 14912888 INFO @ Sat, 15 Jan 2022 17:24:29: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 17:24:29: #1 finished! INFO @ Sat, 15 Jan 2022 17:24:29: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:24:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:24:29: 11000000 INFO @ Sat, 15 Jan 2022 17:24:31: 7000000 INFO @ Sat, 15 Jan 2022 17:24:31: #2 number of paired peaks: 16330 INFO @ Sat, 15 Jan 2022 17:24:31: start model_add_line... INFO @ Sat, 15 Jan 2022 17:24:31: start X-correlation... INFO @ Sat, 15 Jan 2022 17:24:31: end of X-cor INFO @ Sat, 15 Jan 2022 17:24:31: #2 finished! INFO @ Sat, 15 Jan 2022 17:24:31: #2 predicted fragment length is 152 bps INFO @ Sat, 15 Jan 2022 17:24:31: #2 alternative fragment length(s) may be 152 bps INFO @ Sat, 15 Jan 2022 17:24:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX6581723/SRX6581723.05_model.r INFO @ Sat, 15 Jan 2022 17:24:31: #3 Call peaks... INFO @ Sat, 15 Jan 2022 17:24:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 17:24:37: 12000000 INFO @ Sat, 15 Jan 2022 17:24:39: 8000000 INFO @ Sat, 15 Jan 2022 17:24:45: 13000000 INFO @ Sat, 15 Jan 2022 17:24:47: 9000000 INFO @ Sat, 15 Jan 2022 17:24:52: 14000000 INFO @ Sat, 15 Jan 2022 17:24:55: 10000000 INFO @ Sat, 15 Jan 2022 17:24:59: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 17:24:59: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 17:24:59: #1 total tags in treatment: 14913048 INFO @ Sat, 15 Jan 2022 17:24:59: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:24:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 17:25:00: #1 tags after filtering in treatment: 14912888 INFO @ Sat, 15 Jan 2022 17:25:00: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 17:25:00: #1 finished! INFO @ Sat, 15 Jan 2022 17:25:00: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:25:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:25:02: #2 number of paired peaks: 16330 INFO @ Sat, 15 Jan 2022 17:25:02: start model_add_line... INFO @ Sat, 15 Jan 2022 17:25:02: start X-correlation... INFO @ Sat, 15 Jan 2022 17:25:02: end of X-cor INFO @ Sat, 15 Jan 2022 17:25:02: #2 finished! INFO @ Sat, 15 Jan 2022 17:25:02: #2 predicted fragment length is 152 bps INFO @ Sat, 15 Jan 2022 17:25:02: #2 alternative fragment length(s) may be 152 bps INFO @ Sat, 15 Jan 2022 17:25:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX6581723/SRX6581723.10_model.r INFO @ Sat, 15 Jan 2022 17:25:02: #3 Call peaks... INFO @ Sat, 15 Jan 2022 17:25:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 17:25:02: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 17:25:03: 11000000 INFO @ Sat, 15 Jan 2022 17:25:11: 12000000 INFO @ Sat, 15 Jan 2022 17:25:18: 13000000 INFO @ Sat, 15 Jan 2022 17:25:21: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX6581723/SRX6581723.05_peaks.xls INFO @ Sat, 15 Jan 2022 17:25:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX6581723/SRX6581723.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 17:25:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX6581723/SRX6581723.05_summits.bed INFO @ Sat, 15 Jan 2022 17:25:23: Done! pass1 - making usageList (63 chroms): 2 millis pass2 - checking and writing primary data (6260 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 17:25:25: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 17:25:32: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 17:25:32: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 17:25:32: #1 total tags in treatment: 14913048 INFO @ Sat, 15 Jan 2022 17:25:32: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:25:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 17:25:32: #1 tags after filtering in treatment: 14912888 INFO @ Sat, 15 Jan 2022 17:25:32: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 17:25:32: #1 finished! INFO @ Sat, 15 Jan 2022 17:25:32: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:25:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:25:33: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 17:25:34: #2 number of paired peaks: 16330 INFO @ Sat, 15 Jan 2022 17:25:34: start model_add_line... INFO @ Sat, 15 Jan 2022 17:25:34: start X-correlation... INFO @ Sat, 15 Jan 2022 17:25:34: end of X-cor INFO @ Sat, 15 Jan 2022 17:25:34: #2 finished! INFO @ Sat, 15 Jan 2022 17:25:34: #2 predicted fragment length is 152 bps INFO @ Sat, 15 Jan 2022 17:25:34: #2 alternative fragment length(s) may be 152 bps INFO @ Sat, 15 Jan 2022 17:25:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX6581723/SRX6581723.20_model.r INFO @ Sat, 15 Jan 2022 17:25:34: #3 Call peaks... INFO @ Sat, 15 Jan 2022 17:25:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 17:25:52: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX6581723/SRX6581723.10_peaks.xls INFO @ Sat, 15 Jan 2022 17:25:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX6581723/SRX6581723.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 17:25:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX6581723/SRX6581723.10_summits.bed INFO @ Sat, 15 Jan 2022 17:25:52: Done! pass1 - making usageList (46 chroms): 1 millis pass2 - checking and writing primary data (2893 records, 4 fields): 116 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 17:26:05: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 17:26:24: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX6581723/SRX6581723.20_peaks.xls INFO @ Sat, 15 Jan 2022 17:26:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX6581723/SRX6581723.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 17:26:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX6581723/SRX6581723.20_summits.bed INFO @ Sat, 15 Jan 2022 17:26:24: Done! pass1 - making usageList (34 chroms): 1 millis pass2 - checking and writing primary data (853 records, 4 fields): 5 millis CompletedMACS2peakCalling