Job ID = 12531486 SRX = SRX6922980 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 14319167 spots for SRR10202926/SRR10202926.sra Written 14319167 spots for SRR10202926/SRR10202926.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: 00:00:02 Multiseed full-index search: 00:09:36 14319167 reads; of these: 14319167 (100.00%) were unpaired; of these: 3771210 (26.34%) aligned 0 times 7140653 (49.87%) aligned exactly 1 time 3407304 (23.80%) aligned >1 times 73.66% overall alignment rate Time searching: 00:09:41 Overall time: 00:09:41 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] 7144169 / 10547957 = 0.6773 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 17 Apr 2021 07:58:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX6922980/SRX6922980.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX6922980/SRX6922980.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX6922980/SRX6922980.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX6922980/SRX6922980.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, 17 Apr 2021 07:58:21: #1 read tag files... INFO @ Sat, 17 Apr 2021 07:58:21: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 07:58:28: 1000000 INFO @ Sat, 17 Apr 2021 07:58:35: 2000000 INFO @ Sat, 17 Apr 2021 07:58:43: 3000000 INFO @ Sat, 17 Apr 2021 07:58:46: #1 tag size is determined as 75 bps INFO @ Sat, 17 Apr 2021 07:58:46: #1 tag size = 75 INFO @ Sat, 17 Apr 2021 07:58:46: #1 total tags in treatment: 3403788 INFO @ Sat, 17 Apr 2021 07:58:46: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 07:58:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 17 Apr 2021 07:58:46: #1 tags after filtering in treatment: 3403493 INFO @ Sat, 17 Apr 2021 07:58:46: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 17 Apr 2021 07:58:46: #1 finished! INFO @ Sat, 17 Apr 2021 07:58:46: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 07:58:46: #2 looking for paired plus/minus strand peaks... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 17 Apr 2021 07:58:50: #2 number of paired peaks: 54970 INFO @ Sat, 17 Apr 2021 07:58:50: start model_add_line... INFO @ Sat, 17 Apr 2021 07:58:50: start X-correlation... INFO @ Sat, 17 Apr 2021 07:58:50: end of X-cor INFO @ Sat, 17 Apr 2021 07:58:50: #2 finished! INFO @ Sat, 17 Apr 2021 07:58:50: #2 predicted fragment length is 168 bps INFO @ Sat, 17 Apr 2021 07:58:50: #2 alternative fragment length(s) may be 168 bps INFO @ Sat, 17 Apr 2021 07:58:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX6922980/SRX6922980.05_model.r INFO @ Sat, 17 Apr 2021 07:58:50: #3 Call peaks... INFO @ Sat, 17 Apr 2021 07:58:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 07:58:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX6922980/SRX6922980.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX6922980/SRX6922980.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX6922980/SRX6922980.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX6922980/SRX6922980.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, 17 Apr 2021 07:58:51: #1 read tag files... INFO @ Sat, 17 Apr 2021 07:58:51: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 07:58:57: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 07:58:58: 1000000 INFO @ Sat, 17 Apr 2021 07:59:01: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX6922980/SRX6922980.05_peaks.xls INFO @ Sat, 17 Apr 2021 07:59:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX6922980/SRX6922980.05_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 07:59:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX6922980/SRX6922980.05_summits.bed INFO @ Sat, 17 Apr 2021 07:59:01: Done! pass1 - making usageList (39 chroms): 1 millis pass2 - checking and writing primary data (4876 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 17 Apr 2021 07:59:05: 2000000 INFO @ Sat, 17 Apr 2021 07:59:12: 3000000 INFO @ Sat, 17 Apr 2021 07:59:15: #1 tag size is determined as 75 bps INFO @ Sat, 17 Apr 2021 07:59:15: #1 tag size = 75 INFO @ Sat, 17 Apr 2021 07:59:15: #1 total tags in treatment: 3403788 INFO @ Sat, 17 Apr 2021 07:59:15: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 07:59:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 17 Apr 2021 07:59:15: #1 tags after filtering in treatment: 3403493 INFO @ Sat, 17 Apr 2021 07:59:15: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 17 Apr 2021 07:59:15: #1 finished! INFO @ Sat, 17 Apr 2021 07:59:15: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 07:59:15: #2 looking for paired plus/minus strand peaks... BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 17 Apr 2021 07:59:19: #2 number of paired peaks: 54970 INFO @ Sat, 17 Apr 2021 07:59:19: start model_add_line... INFO @ Sat, 17 Apr 2021 07:59:19: start X-correlation... INFO @ Sat, 17 Apr 2021 07:59:19: end of X-cor INFO @ Sat, 17 Apr 2021 07:59:19: #2 finished! INFO @ Sat, 17 Apr 2021 07:59:19: #2 predicted fragment length is 168 bps INFO @ Sat, 17 Apr 2021 07:59:19: #2 alternative fragment length(s) may be 168 bps INFO @ Sat, 17 Apr 2021 07:59:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX6922980/SRX6922980.10_model.r INFO @ Sat, 17 Apr 2021 07:59:19: #3 Call peaks... INFO @ Sat, 17 Apr 2021 07:59:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 07:59:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX6922980/SRX6922980.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX6922980/SRX6922980.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX6922980/SRX6922980.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX6922980/SRX6922980.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, 17 Apr 2021 07:59:21: #1 read tag files... INFO @ Sat, 17 Apr 2021 07:59:21: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 07:59:26: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 07:59:29: 1000000 INFO @ Sat, 17 Apr 2021 07:59:30: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX6922980/SRX6922980.10_peaks.xls INFO @ Sat, 17 Apr 2021 07:59:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX6922980/SRX6922980.10_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 07:59:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX6922980/SRX6922980.10_summits.bed INFO @ Sat, 17 Apr 2021 07:59:30: Done! pass1 - making usageList (27 chroms): 1 millis pass2 - checking and writing primary data (1203 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 17 Apr 2021 07:59:36: 2000000 INFO @ Sat, 17 Apr 2021 07:59:44: 3000000 INFO @ Sat, 17 Apr 2021 07:59:47: #1 tag size is determined as 75 bps INFO @ Sat, 17 Apr 2021 07:59:47: #1 tag size = 75 INFO @ Sat, 17 Apr 2021 07:59:47: #1 total tags in treatment: 3403788 INFO @ Sat, 17 Apr 2021 07:59:47: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 07:59:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 17 Apr 2021 07:59:47: #1 tags after filtering in treatment: 3403493 INFO @ Sat, 17 Apr 2021 07:59:47: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 17 Apr 2021 07:59:47: #1 finished! INFO @ Sat, 17 Apr 2021 07:59:47: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 07:59:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 07:59:51: #2 number of paired peaks: 54970 INFO @ Sat, 17 Apr 2021 07:59:51: start model_add_line... INFO @ Sat, 17 Apr 2021 07:59:51: start X-correlation... INFO @ Sat, 17 Apr 2021 07:59:51: end of X-cor INFO @ Sat, 17 Apr 2021 07:59:51: #2 finished! INFO @ Sat, 17 Apr 2021 07:59:51: #2 predicted fragment length is 168 bps INFO @ Sat, 17 Apr 2021 07:59:51: #2 alternative fragment length(s) may be 168 bps INFO @ Sat, 17 Apr 2021 07:59:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX6922980/SRX6922980.20_model.r INFO @ Sat, 17 Apr 2021 07:59:51: #3 Call peaks... INFO @ Sat, 17 Apr 2021 07:59:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 07:59:58: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 17 Apr 2021 08:00:02: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX6922980/SRX6922980.20_peaks.xls INFO @ Sat, 17 Apr 2021 08:00:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX6922980/SRX6922980.20_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 08:00:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX6922980/SRX6922980.20_summits.bed INFO @ Sat, 17 Apr 2021 08:00:02: Done! pass1 - making usageList (21 chroms): 1 millis pass2 - checking and writing primary data (88 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。