Job ID = 14518039 SRX = SRX10533685 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 4000000 spots for SRR14165486/SRR14165486.sra Written 4000000 spots for SRR14165486/SRR14165486.sra Read 4000000 spots for SRR14165487/SRR14165487.sra Written 4000000 spots for SRR14165487/SRR14165487.sra Read 4000000 spots for SRR14165488/SRR14165488.sra Written 4000000 spots for SRR14165488/SRR14165488.sra Read 4000000 spots for SRR14165489/SRR14165489.sra Written 4000000 spots for SRR14165489/SRR14165489.sra 2022-01-14T22:50:44 prefetch.2.10.7: 1) Downloading 'SRR14165490'... 2022-01-14T22:50:44 prefetch.2.10.7: Downloading via HTTPS... 2022-01-14T22:50:55 prefetch.2.10.7: HTTPS download succeed 2022-01-14T22:50:56 prefetch.2.10.7: 'SRR14165490' is valid 2022-01-14T22:50:56 prefetch.2.10.7: 1) 'SRR14165490' was downloaded successfully 2022-01-14T22:50:56 prefetch.2.10.7: 'SRR14165490' has 0 unresolved dependencies Read 4000000 spots for SRR14165490/SRR14165490.sra Written 4000000 spots for SRR14165490/SRR14165490.sra Read 4000000 spots for SRR14165491/SRR14165491.sra Written 4000000 spots for SRR14165491/SRR14165491.sra Read 2396228 spots for SRR14165492/SRR14165492.sra Written 2396228 spots for SRR14165492/SRR14165492.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:51 26396228 reads; of these: 26396228 (100.00%) were unpaired; of these: 13841921 (52.44%) aligned 0 times 10121162 (38.34%) aligned exactly 1 time 2433145 (9.22%) aligned >1 times 47.56% overall alignment rate Time searching: 00:07:54 Overall time: 00:07:54 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 8 files... [bam_rmdupse_core] 3633166 / 12554307 = 0.2894 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 08:03:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX10533685/SRX10533685.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX10533685/SRX10533685.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX10533685/SRX10533685.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX10533685/SRX10533685.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 08:03:08: #1 read tag files... INFO @ Sat, 15 Jan 2022 08:03:08: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 08:03:14: 1000000 INFO @ Sat, 15 Jan 2022 08:03:20: 2000000 INFO @ Sat, 15 Jan 2022 08:03:27: 3000000 INFO @ Sat, 15 Jan 2022 08:03:33: 4000000 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 08:03:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX10533685/SRX10533685.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX10533685/SRX10533685.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX10533685/SRX10533685.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX10533685/SRX10533685.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 08:03:37: #1 read tag files... INFO @ Sat, 15 Jan 2022 08:03:37: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 08:03:39: 5000000 INFO @ Sat, 15 Jan 2022 08:03:44: 1000000 INFO @ Sat, 15 Jan 2022 08:03:46: 6000000 INFO @ Sat, 15 Jan 2022 08:03:51: 2000000 INFO @ Sat, 15 Jan 2022 08:03:53: 7000000 INFO @ Sat, 15 Jan 2022 08:03:58: 3000000 INFO @ Sat, 15 Jan 2022 08:04:00: 8000000 INFO @ Sat, 15 Jan 2022 08:04:05: 4000000 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 08:04:06: #1 tag size is determined as 51 bps INFO @ Sat, 15 Jan 2022 08:04:06: #1 tag size = 51 INFO @ Sat, 15 Jan 2022 08:04:06: #1 total tags in treatment: 8921141 INFO @ Sat, 15 Jan 2022 08:04:06: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 08:04:06: #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 08:04:06: #1 tags after filtering in treatment: 8920923 INFO @ Sat, 15 Jan 2022 08:04:06: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 08:04:06: #1 finished! INFO @ Sat, 15 Jan 2022 08:04:06: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 08:04:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 08:04:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX10533685/SRX10533685.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX10533685/SRX10533685.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX10533685/SRX10533685.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX10533685/SRX10533685.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 08:04:07: #1 read tag files... INFO @ Sat, 15 Jan 2022 08:04:07: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 08:04:09: #2 number of paired peaks: 56835 INFO @ Sat, 15 Jan 2022 08:04:09: start model_add_line... INFO @ Sat, 15 Jan 2022 08:04:09: start X-correlation... INFO @ Sat, 15 Jan 2022 08:04:09: end of X-cor INFO @ Sat, 15 Jan 2022 08:04:09: #2 finished! INFO @ Sat, 15 Jan 2022 08:04:09: #2 predicted fragment length is 297 bps INFO @ Sat, 15 Jan 2022 08:04:09: #2 alternative fragment length(s) may be 297 bps INFO @ Sat, 15 Jan 2022 08:04:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX10533685/SRX10533685.05_model.r INFO @ Sat, 15 Jan 2022 08:04:09: #3 Call peaks... INFO @ Sat, 15 Jan 2022 08:04:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 08:04:12: 5000000 INFO @ Sat, 15 Jan 2022 08:04:14: 1000000 INFO @ Sat, 15 Jan 2022 08:04:18: 6000000 INFO @ Sat, 15 Jan 2022 08:04:22: 2000000 INFO @ Sat, 15 Jan 2022 08:04:25: 7000000 INFO @ Sat, 15 Jan 2022 08:04:29: 3000000 INFO @ Sat, 15 Jan 2022 08:04:32: 8000000 INFO @ Sat, 15 Jan 2022 08:04:33: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 08:04:36: 4000000 INFO @ Sat, 15 Jan 2022 08:04:39: #1 tag size is determined as 51 bps INFO @ Sat, 15 Jan 2022 08:04:39: #1 tag size = 51 INFO @ Sat, 15 Jan 2022 08:04:39: #1 total tags in treatment: 8921141 INFO @ Sat, 15 Jan 2022 08:04:39: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 08:04:39: #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 08:04:39: #1 tags after filtering in treatment: 8920923 INFO @ Sat, 15 Jan 2022 08:04:39: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 08:04:39: #1 finished! INFO @ Sat, 15 Jan 2022 08:04:39: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 08:04:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 08:04:42: #2 number of paired peaks: 56835 INFO @ Sat, 15 Jan 2022 08:04:42: start model_add_line... INFO @ Sat, 15 Jan 2022 08:04:42: start X-correlation... INFO @ Sat, 15 Jan 2022 08:04:42: end of X-cor INFO @ Sat, 15 Jan 2022 08:04:42: #2 finished! INFO @ Sat, 15 Jan 2022 08:04:42: #2 predicted fragment length is 297 bps INFO @ Sat, 15 Jan 2022 08:04:42: #2 alternative fragment length(s) may be 297 bps INFO @ Sat, 15 Jan 2022 08:04:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX10533685/SRX10533685.10_model.r INFO @ Sat, 15 Jan 2022 08:04:42: #3 Call peaks... INFO @ Sat, 15 Jan 2022 08:04:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 08:04:42: 5000000 INFO @ Sat, 15 Jan 2022 08:04:44: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX10533685/SRX10533685.05_peaks.xls INFO @ Sat, 15 Jan 2022 08:04:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX10533685/SRX10533685.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 08:04:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX10533685/SRX10533685.05_summits.bed INFO @ Sat, 15 Jan 2022 08:04:44: Done! pass1 - making usageList (60 chroms): 1 millis pass2 - checking and writing primary data (1749 records, 4 fields): 33 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 08:04:49: 6000000 INFO @ Sat, 15 Jan 2022 08:04:55: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 08:05:02: 8000000 INFO @ Sat, 15 Jan 2022 08:05:05: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 08:05:08: #1 tag size is determined as 51 bps INFO @ Sat, 15 Jan 2022 08:05:08: #1 tag size = 51 INFO @ Sat, 15 Jan 2022 08:05:08: #1 total tags in treatment: 8921141 INFO @ Sat, 15 Jan 2022 08:05:08: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 08:05:08: #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 08:05:08: #1 tags after filtering in treatment: 8920923 INFO @ Sat, 15 Jan 2022 08:05:08: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 08:05:08: #1 finished! INFO @ Sat, 15 Jan 2022 08:05:08: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 08:05:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 08:05:10: #2 number of paired peaks: 56835 INFO @ Sat, 15 Jan 2022 08:05:10: start model_add_line... INFO @ Sat, 15 Jan 2022 08:05:11: start X-correlation... INFO @ Sat, 15 Jan 2022 08:05:11: end of X-cor INFO @ Sat, 15 Jan 2022 08:05:11: #2 finished! INFO @ Sat, 15 Jan 2022 08:05:11: #2 predicted fragment length is 297 bps INFO @ Sat, 15 Jan 2022 08:05:11: #2 alternative fragment length(s) may be 297 bps INFO @ Sat, 15 Jan 2022 08:05:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX10533685/SRX10533685.20_model.r INFO @ Sat, 15 Jan 2022 08:05:11: #3 Call peaks... INFO @ Sat, 15 Jan 2022 08:05:11: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 08:05:16: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX10533685/SRX10533685.10_peaks.xls INFO @ Sat, 15 Jan 2022 08:05:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX10533685/SRX10533685.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 08:05:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX10533685/SRX10533685.10_summits.bed INFO @ Sat, 15 Jan 2022 08:05:16: Done! pass1 - making usageList (49 chroms): 1 millis pass2 - checking and writing primary data (703 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 08:05:34: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 08:05:45: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX10533685/SRX10533685.20_peaks.xls INFO @ Sat, 15 Jan 2022 08:05:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX10533685/SRX10533685.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 08:05:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX10533685/SRX10533685.20_summits.bed INFO @ Sat, 15 Jan 2022 08:05:45: Done! pass1 - making usageList (35 chroms): 1 millis pass2 - checking and writing primary data (251 records, 4 fields): 2 millis CompletedMACS2peakCalling