Job ID = 14518155 SRX = SRX9430824 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 6366183 spots for SRR12978976/SRR12978976.sra Written 6366183 spots for SRR12978976/SRR12978976.sra Read 7835925 spots for SRR12978977/SRR12978977.sra Written 7835925 spots for SRR12978977/SRR12978977.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: 00:00:03 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:23:04 14202108 reads; of these: 14202108 (100.00%) were unpaired; of these: 7428527 (52.31%) aligned 0 times 4594259 (32.35%) aligned exactly 1 time 2179322 (15.35%) aligned >1 times 47.69% overall alignment rate Time searching: 00:23:09 Overall time: 00:23:09 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] 1831841 / 6773581 = 0.2704 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 10:43:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX9430824/SRX9430824.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX9430824/SRX9430824.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX9430824/SRX9430824.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX9430824/SRX9430824.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 10:43:54: #1 read tag files... INFO @ Sat, 15 Jan 2022 10:43:54: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 10:44:02: 1000000 INFO @ Sat, 15 Jan 2022 10:44:12: 2000000 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 10:44:22: 3000000 INFO @ Sat, 15 Jan 2022 10:44:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX9430824/SRX9430824.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX9430824/SRX9430824.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX9430824/SRX9430824.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX9430824/SRX9430824.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 10:44:24: #1 read tag files... INFO @ Sat, 15 Jan 2022 10:44:24: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 10:44:31: 4000000 INFO @ Sat, 15 Jan 2022 10:44:33: 1000000 INFO @ Sat, 15 Jan 2022 10:44:41: #1 tag size is determined as 57 bps INFO @ Sat, 15 Jan 2022 10:44:41: #1 tag size = 57 INFO @ Sat, 15 Jan 2022 10:44:41: #1 total tags in treatment: 4941740 INFO @ Sat, 15 Jan 2022 10:44:41: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 10:44:41: #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 10:44:41: #1 tags after filtering in treatment: 4941504 INFO @ Sat, 15 Jan 2022 10:44:41: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 10:44:41: #1 finished! INFO @ Sat, 15 Jan 2022 10:44:41: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 10:44:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 10:44:42: 2000000 INFO @ Sat, 15 Jan 2022 10:44:44: #2 number of paired peaks: 55093 INFO @ Sat, 15 Jan 2022 10:44:44: start model_add_line... INFO @ Sat, 15 Jan 2022 10:44:44: start X-correlation... INFO @ Sat, 15 Jan 2022 10:44:44: end of X-cor INFO @ Sat, 15 Jan 2022 10:44:44: #2 finished! INFO @ Sat, 15 Jan 2022 10:44:44: #2 predicted fragment length is 125 bps INFO @ Sat, 15 Jan 2022 10:44:44: #2 alternative fragment length(s) may be 125 bps INFO @ Sat, 15 Jan 2022 10:44:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX9430824/SRX9430824.05_model.r INFO @ Sat, 15 Jan 2022 10:44:44: #3 Call peaks... INFO @ Sat, 15 Jan 2022 10:44:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 10:44:50: 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 10:44:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX9430824/SRX9430824.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX9430824/SRX9430824.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX9430824/SRX9430824.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX9430824/SRX9430824.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 10:44:54: #1 read tag files... INFO @ Sat, 15 Jan 2022 10:44:54: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 10:44:55: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 10:44:58: 4000000 INFO @ Sat, 15 Jan 2022 10:45:01: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX9430824/SRX9430824.05_peaks.xls INFO @ Sat, 15 Jan 2022 10:45:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX9430824/SRX9430824.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 10:45:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX9430824/SRX9430824.05_summits.bed INFO @ Sat, 15 Jan 2022 10:45:01: Done! pass1 - making usageList (76 chroms): 2 millis pass2 - checking and writing primary data (3710 records, 4 fields): 34 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 10:45:03: 1000000 INFO @ Sat, 15 Jan 2022 10:45:07: #1 tag size is determined as 57 bps INFO @ Sat, 15 Jan 2022 10:45:07: #1 tag size = 57 INFO @ Sat, 15 Jan 2022 10:45:07: #1 total tags in treatment: 4941740 INFO @ Sat, 15 Jan 2022 10:45:07: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 10:45:07: #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 10:45:07: #1 tags after filtering in treatment: 4941504 INFO @ Sat, 15 Jan 2022 10:45:07: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 10:45:07: #1 finished! INFO @ Sat, 15 Jan 2022 10:45:07: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 10:45:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 10:45:11: #2 number of paired peaks: 55093 INFO @ Sat, 15 Jan 2022 10:45:11: start model_add_line... INFO @ Sat, 15 Jan 2022 10:45:11: start X-correlation... INFO @ Sat, 15 Jan 2022 10:45:11: end of X-cor INFO @ Sat, 15 Jan 2022 10:45:11: #2 finished! INFO @ Sat, 15 Jan 2022 10:45:11: #2 predicted fragment length is 125 bps INFO @ Sat, 15 Jan 2022 10:45:11: #2 alternative fragment length(s) may be 125 bps INFO @ Sat, 15 Jan 2022 10:45:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX9430824/SRX9430824.10_model.r INFO @ Sat, 15 Jan 2022 10:45:11: #3 Call peaks... INFO @ Sat, 15 Jan 2022 10:45:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 10:45:12: 2000000 INFO @ Sat, 15 Jan 2022 10:45:20: 3000000 INFO @ Sat, 15 Jan 2022 10:45:21: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 10:45:27: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX9430824/SRX9430824.10_peaks.xls INFO @ Sat, 15 Jan 2022 10:45:28: 4000000 INFO @ Sat, 15 Jan 2022 10:45:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX9430824/SRX9430824.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 10:45:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX9430824/SRX9430824.10_summits.bed INFO @ Sat, 15 Jan 2022 10:45:28: Done! pass1 - making usageList (54 chroms): 1 millis pass2 - checking and writing primary data (915 records, 4 fields): 34 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 10:45:35: #1 tag size is determined as 57 bps INFO @ Sat, 15 Jan 2022 10:45:35: #1 tag size = 57 INFO @ Sat, 15 Jan 2022 10:45:35: #1 total tags in treatment: 4941740 INFO @ Sat, 15 Jan 2022 10:45:35: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 10:45:35: #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 10:45:36: #1 tags after filtering in treatment: 4941504 INFO @ Sat, 15 Jan 2022 10:45:36: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 10:45:36: #1 finished! INFO @ Sat, 15 Jan 2022 10:45:36: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 10:45:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 10:45:39: #2 number of paired peaks: 55093 INFO @ Sat, 15 Jan 2022 10:45:39: start model_add_line... INFO @ Sat, 15 Jan 2022 10:45:39: start X-correlation... INFO @ Sat, 15 Jan 2022 10:45:39: end of X-cor INFO @ Sat, 15 Jan 2022 10:45:39: #2 finished! INFO @ Sat, 15 Jan 2022 10:45:39: #2 predicted fragment length is 125 bps INFO @ Sat, 15 Jan 2022 10:45:39: #2 alternative fragment length(s) may be 125 bps INFO @ Sat, 15 Jan 2022 10:45:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX9430824/SRX9430824.20_model.r INFO @ Sat, 15 Jan 2022 10:45:39: #3 Call peaks... INFO @ Sat, 15 Jan 2022 10:45:39: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 10:45:49: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 10:45:55: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX9430824/SRX9430824.20_peaks.xls INFO @ Sat, 15 Jan 2022 10:45:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX9430824/SRX9430824.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 10:45:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX9430824/SRX9430824.20_summits.bed INFO @ Sat, 15 Jan 2022 10:45:55: Done! pass1 - making usageList (46 chroms): 1 millis pass2 - checking and writing primary data (282 records, 4 fields): 39 millis CompletedMACS2peakCalling