Job ID = 14518167 SRX = SRX9430836 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 5914893 spots for SRR12978999/SRR12978999.sra Written 5914893 spots for SRR12978999/SRR12978999.sra Read 6010074 spots for SRR12979000/SRR12979000.sra Written 6010074 spots for SRR12979000/SRR12979000.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:32:14 11924967 reads; of these: 11924967 (100.00%) were unpaired; of these: 1961295 (16.45%) aligned 0 times 6122820 (51.34%) aligned exactly 1 time 3840852 (32.21%) aligned >1 times 83.55% overall alignment rate Time searching: 00:32:19 Overall time: 00:32:19 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_rmdupse_core] 1402570 / 9963672 = 0.1408 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 11:06:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX9430836/SRX9430836.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX9430836/SRX9430836.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX9430836/SRX9430836.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX9430836/SRX9430836.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 11:06:19: #1 read tag files... INFO @ Sat, 15 Jan 2022 11:06:19: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 11:06:24: 1000000 INFO @ Sat, 15 Jan 2022 11:06:29: 2000000 INFO @ Sat, 15 Jan 2022 11:06:34: 3000000 INFO @ Sat, 15 Jan 2022 11:06:39: 4000000 INFO @ Sat, 15 Jan 2022 11:06:44: 5000000 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 11:06:49: 6000000 INFO @ Sat, 15 Jan 2022 11:06:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX9430836/SRX9430836.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX9430836/SRX9430836.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX9430836/SRX9430836.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX9430836/SRX9430836.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 11:06:49: #1 read tag files... INFO @ Sat, 15 Jan 2022 11:06:49: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 11:06:53: 7000000 INFO @ Sat, 15 Jan 2022 11:06:54: 1000000 INFO @ Sat, 15 Jan 2022 11:06:58: 8000000 INFO @ Sat, 15 Jan 2022 11:06:59: 2000000 INFO @ Sat, 15 Jan 2022 11:07:01: #1 tag size is determined as 53 bps INFO @ Sat, 15 Jan 2022 11:07:01: #1 tag size = 53 INFO @ Sat, 15 Jan 2022 11:07:01: #1 total tags in treatment: 8561102 INFO @ Sat, 15 Jan 2022 11:07:01: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 11:07:01: #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 11:07:02: #1 tags after filtering in treatment: 8560898 INFO @ Sat, 15 Jan 2022 11:07:02: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 11:07:02: #1 finished! INFO @ Sat, 15 Jan 2022 11:07:02: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 11:07:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 11:07:04: #2 number of paired peaks: 34217 INFO @ Sat, 15 Jan 2022 11:07:04: start model_add_line... INFO @ Sat, 15 Jan 2022 11:07:04: start X-correlation... INFO @ Sat, 15 Jan 2022 11:07:04: end of X-cor INFO @ Sat, 15 Jan 2022 11:07:04: #2 finished! INFO @ Sat, 15 Jan 2022 11:07:04: #2 predicted fragment length is 129 bps INFO @ Sat, 15 Jan 2022 11:07:04: #2 alternative fragment length(s) may be 129 bps INFO @ Sat, 15 Jan 2022 11:07:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX9430836/SRX9430836.05_model.r INFO @ Sat, 15 Jan 2022 11:07:04: #3 Call peaks... INFO @ Sat, 15 Jan 2022 11:07:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 11:07:04: 3000000 INFO @ Sat, 15 Jan 2022 11:07:09: 4000000 INFO @ Sat, 15 Jan 2022 11:07:14: 5000000 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 11:07:18: 6000000 INFO @ Sat, 15 Jan 2022 11:07:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX9430836/SRX9430836.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX9430836/SRX9430836.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX9430836/SRX9430836.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX9430836/SRX9430836.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 11:07:19: #1 read tag files... INFO @ Sat, 15 Jan 2022 11:07:19: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 11:07:22: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 11:07:23: 7000000 INFO @ Sat, 15 Jan 2022 11:07:24: 1000000 INFO @ Sat, 15 Jan 2022 11:07:28: 8000000 INFO @ Sat, 15 Jan 2022 11:07:29: 2000000 INFO @ Sat, 15 Jan 2022 11:07:31: #1 tag size is determined as 53 bps INFO @ Sat, 15 Jan 2022 11:07:31: #1 tag size = 53 INFO @ Sat, 15 Jan 2022 11:07:31: #1 total tags in treatment: 8561102 INFO @ Sat, 15 Jan 2022 11:07:31: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 11:07:31: #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 11:07:31: #1 tags after filtering in treatment: 8560898 INFO @ Sat, 15 Jan 2022 11:07:31: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 11:07:31: #1 finished! INFO @ Sat, 15 Jan 2022 11:07:31: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 11:07:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 11:07:32: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX9430836/SRX9430836.05_peaks.xls INFO @ Sat, 15 Jan 2022 11:07:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX9430836/SRX9430836.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 11:07:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX9430836/SRX9430836.05_summits.bed INFO @ Sat, 15 Jan 2022 11:07:32: Done! pass1 - making usageList (91 chroms): 2 millis pass2 - checking and writing primary data (9769 records, 4 fields): 52 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 11:07:33: #2 number of paired peaks: 34217 INFO @ Sat, 15 Jan 2022 11:07:33: start model_add_line... INFO @ Sat, 15 Jan 2022 11:07:33: start X-correlation... INFO @ Sat, 15 Jan 2022 11:07:33: end of X-cor INFO @ Sat, 15 Jan 2022 11:07:33: #2 finished! INFO @ Sat, 15 Jan 2022 11:07:33: #2 predicted fragment length is 129 bps INFO @ Sat, 15 Jan 2022 11:07:33: #2 alternative fragment length(s) may be 129 bps INFO @ Sat, 15 Jan 2022 11:07:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX9430836/SRX9430836.10_model.r INFO @ Sat, 15 Jan 2022 11:07:33: #3 Call peaks... INFO @ Sat, 15 Jan 2022 11:07:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 11:07:34: 3000000 INFO @ Sat, 15 Jan 2022 11:07:39: 4000000 INFO @ Sat, 15 Jan 2022 11:07:44: 5000000 INFO @ Sat, 15 Jan 2022 11:07:49: 6000000 INFO @ Sat, 15 Jan 2022 11:07:52: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 11:07:54: 7000000 INFO @ Sat, 15 Jan 2022 11:07:59: 8000000 INFO @ Sat, 15 Jan 2022 11:08:02: #1 tag size is determined as 53 bps INFO @ Sat, 15 Jan 2022 11:08:02: #1 tag size = 53 INFO @ Sat, 15 Jan 2022 11:08:02: #1 total tags in treatment: 8561102 INFO @ Sat, 15 Jan 2022 11:08:02: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 11:08:02: #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 11:08:02: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX9430836/SRX9430836.10_peaks.xls INFO @ Sat, 15 Jan 2022 11:08:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX9430836/SRX9430836.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 11:08:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX9430836/SRX9430836.10_summits.bed INFO @ Sat, 15 Jan 2022 11:08:02: #1 tags after filtering in treatment: 8560898 INFO @ Sat, 15 Jan 2022 11:08:02: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 11:08:02: #1 finished! INFO @ Sat, 15 Jan 2022 11:08:02: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 11:08:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 11:08:03: Done! pass1 - making usageList (49 chroms): 1 millis pass2 - checking and writing primary data (2390 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 11:08:04: #2 number of paired peaks: 34217 INFO @ Sat, 15 Jan 2022 11:08:04: start model_add_line... INFO @ Sat, 15 Jan 2022 11:08:04: start X-correlation... INFO @ Sat, 15 Jan 2022 11:08:04: end of X-cor INFO @ Sat, 15 Jan 2022 11:08:04: #2 finished! INFO @ Sat, 15 Jan 2022 11:08:04: #2 predicted fragment length is 129 bps INFO @ Sat, 15 Jan 2022 11:08:04: #2 alternative fragment length(s) may be 129 bps INFO @ Sat, 15 Jan 2022 11:08:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX9430836/SRX9430836.20_model.r INFO @ Sat, 15 Jan 2022 11:08:04: #3 Call peaks... INFO @ Sat, 15 Jan 2022 11:08:04: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 11:08:23: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 11:08:33: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX9430836/SRX9430836.20_peaks.xls INFO @ Sat, 15 Jan 2022 11:08:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX9430836/SRX9430836.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 11:08:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX9430836/SRX9430836.20_summits.bed INFO @ Sat, 15 Jan 2022 11:08:33: Done! pass1 - making usageList (34 chroms): 1 millis pass2 - checking and writing primary data (612 records, 4 fields): 281 millis CompletedMACS2peakCalling