Job ID = 12531489 SRX = SRX8142330 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 7210159 spots for SRR11574129/SRR11574129.sra Written 7210159 spots for SRR11574129/SRR11574129.sra Read 7093912 spots for SRR11574130/SRR11574130.sra Written 7093912 spots for SRR11574130/SRR11574130.sra Read 7185891 spots for SRR11574131/SRR11574131.sra Written 7185891 spots for SRR11574131/SRR11574131.sra Read 7057565 spots for SRR11574132/SRR11574132.sra Written 7057565 spots for SRR11574132/SRR11574132.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: 00:14:20 28547527 reads; of these: 28547527 (100.00%) were unpaired; of these: 19293934 (67.59%) aligned 0 times 6347706 (22.24%) aligned exactly 1 time 2905887 (10.18%) aligned >1 times 32.41% overall alignment rate Time searching: 00:14:25 Overall time: 00:14:25 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] 4040802 / 9253593 = 0.4367 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 08:05:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8142330/SRX8142330.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8142330/SRX8142330.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8142330/SRX8142330.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8142330/SRX8142330.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 08:05:25: #1 read tag files... INFO @ Sat, 17 Apr 2021 08:05:25: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 08:05:36: 1000000 INFO @ Sat, 17 Apr 2021 08:05:46: 2000000 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 08:05:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8142330/SRX8142330.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8142330/SRX8142330.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8142330/SRX8142330.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8142330/SRX8142330.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 08:05:56: #1 read tag files... INFO @ Sat, 17 Apr 2021 08:05:56: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 08:05:56: 3000000 INFO @ Sat, 17 Apr 2021 08:06:05: 1000000 INFO @ Sat, 17 Apr 2021 08:06:06: 4000000 INFO @ Sat, 17 Apr 2021 08:06:14: 2000000 INFO @ Sat, 17 Apr 2021 08:06:16: 5000000 INFO @ Sat, 17 Apr 2021 08:06:18: #1 tag size is determined as 84 bps INFO @ Sat, 17 Apr 2021 08:06:18: #1 tag size = 84 INFO @ Sat, 17 Apr 2021 08:06:18: #1 total tags in treatment: 5212791 INFO @ Sat, 17 Apr 2021 08:06:18: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 08:06:18: #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 08:06:19: #1 tags after filtering in treatment: 5212557 INFO @ Sat, 17 Apr 2021 08:06:19: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 17 Apr 2021 08:06:19: #1 finished! INFO @ Sat, 17 Apr 2021 08:06:19: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 08:06:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 08:06:20: #2 number of paired peaks: 8727 INFO @ Sat, 17 Apr 2021 08:06:20: start model_add_line... INFO @ Sat, 17 Apr 2021 08:06:20: start X-correlation... INFO @ Sat, 17 Apr 2021 08:06:20: end of X-cor INFO @ Sat, 17 Apr 2021 08:06:20: #2 finished! INFO @ Sat, 17 Apr 2021 08:06:20: #2 predicted fragment length is 93 bps INFO @ Sat, 17 Apr 2021 08:06:20: #2 alternative fragment length(s) may be 93 bps INFO @ Sat, 17 Apr 2021 08:06:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8142330/SRX8142330.05_model.r WARNING @ Sat, 17 Apr 2021 08:06:20: #2 Since the d (93) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 08:06:20: #2 You may need to consider one of the other alternative d(s): 93 WARNING @ Sat, 17 Apr 2021 08:06:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 17 Apr 2021 08:06:20: #3 Call peaks... INFO @ Sat, 17 Apr 2021 08:06:20: #3 Pre-compute pvalue-qvalue table... 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 08:06:24: 3000000 INFO @ Sat, 17 Apr 2021 08:06:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8142330/SRX8142330.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8142330/SRX8142330.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8142330/SRX8142330.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8142330/SRX8142330.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 08:06:26: #1 read tag files... INFO @ Sat, 17 Apr 2021 08:06:26: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 08:06:31: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 08:06:33: 4000000 INFO @ Sat, 17 Apr 2021 08:06:35: 1000000 INFO @ Sat, 17 Apr 2021 08:06:36: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8142330/SRX8142330.05_peaks.xls INFO @ Sat, 17 Apr 2021 08:06:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8142330/SRX8142330.05_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 08:06:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8142330/SRX8142330.05_summits.bed INFO @ Sat, 17 Apr 2021 08:06:37: Done! pass1 - making usageList (31 chroms): 1 millis pass2 - checking and writing primary data (382 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 17 Apr 2021 08:06:43: 5000000 INFO @ Sat, 17 Apr 2021 08:06:45: #1 tag size is determined as 84 bps INFO @ Sat, 17 Apr 2021 08:06:45: #1 tag size = 84 INFO @ Sat, 17 Apr 2021 08:06:45: #1 total tags in treatment: 5212791 INFO @ Sat, 17 Apr 2021 08:06:45: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 08:06:45: #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 08:06:45: 2000000 INFO @ Sat, 17 Apr 2021 08:06:46: #1 tags after filtering in treatment: 5212557 INFO @ Sat, 17 Apr 2021 08:06:46: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 17 Apr 2021 08:06:46: #1 finished! INFO @ Sat, 17 Apr 2021 08:06:46: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 08:06:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 08:06:47: #2 number of paired peaks: 8727 INFO @ Sat, 17 Apr 2021 08:06:47: start model_add_line... INFO @ Sat, 17 Apr 2021 08:06:47: start X-correlation... INFO @ Sat, 17 Apr 2021 08:06:47: end of X-cor INFO @ Sat, 17 Apr 2021 08:06:47: #2 finished! INFO @ Sat, 17 Apr 2021 08:06:47: #2 predicted fragment length is 93 bps INFO @ Sat, 17 Apr 2021 08:06:47: #2 alternative fragment length(s) may be 93 bps INFO @ Sat, 17 Apr 2021 08:06:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8142330/SRX8142330.10_model.r WARNING @ Sat, 17 Apr 2021 08:06:47: #2 Since the d (93) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 08:06:47: #2 You may need to consider one of the other alternative d(s): 93 WARNING @ Sat, 17 Apr 2021 08:06:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 17 Apr 2021 08:06:47: #3 Call peaks... INFO @ Sat, 17 Apr 2021 08:06:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 08:06:56: 3000000 INFO @ Sat, 17 Apr 2021 08:06:58: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 08:07:04: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8142330/SRX8142330.10_peaks.xls INFO @ Sat, 17 Apr 2021 08:07:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8142330/SRX8142330.10_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 08:07:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8142330/SRX8142330.10_summits.bed INFO @ Sat, 17 Apr 2021 08:07:04: Done! pass1 - making usageList (26 chroms): 1 millis pass2 - checking and writing primary data (191 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 17 Apr 2021 08:07:06: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 17 Apr 2021 08:07:16: 5000000 INFO @ Sat, 17 Apr 2021 08:07:18: #1 tag size is determined as 84 bps INFO @ Sat, 17 Apr 2021 08:07:18: #1 tag size = 84 INFO @ Sat, 17 Apr 2021 08:07:18: #1 total tags in treatment: 5212791 INFO @ Sat, 17 Apr 2021 08:07:18: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 08:07:18: #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 08:07:18: #1 tags after filtering in treatment: 5212557 INFO @ Sat, 17 Apr 2021 08:07:18: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 17 Apr 2021 08:07:18: #1 finished! INFO @ Sat, 17 Apr 2021 08:07:18: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 08:07:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 08:07:20: #2 number of paired peaks: 8727 INFO @ Sat, 17 Apr 2021 08:07:20: start model_add_line... INFO @ Sat, 17 Apr 2021 08:07:20: start X-correlation... INFO @ Sat, 17 Apr 2021 08:07:20: end of X-cor INFO @ Sat, 17 Apr 2021 08:07:20: #2 finished! INFO @ Sat, 17 Apr 2021 08:07:20: #2 predicted fragment length is 93 bps INFO @ Sat, 17 Apr 2021 08:07:20: #2 alternative fragment length(s) may be 93 bps INFO @ Sat, 17 Apr 2021 08:07:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8142330/SRX8142330.20_model.r WARNING @ Sat, 17 Apr 2021 08:07:20: #2 Since the d (93) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 08:07:20: #2 You may need to consider one of the other alternative d(s): 93 WARNING @ Sat, 17 Apr 2021 08:07:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 17 Apr 2021 08:07:20: #3 Call peaks... INFO @ Sat, 17 Apr 2021 08:07:20: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 17 Apr 2021 08:07:31: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 08:07:36: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8142330/SRX8142330.20_peaks.xls INFO @ Sat, 17 Apr 2021 08:07:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8142330/SRX8142330.20_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 08:07:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8142330/SRX8142330.20_summits.bed INFO @ Sat, 17 Apr 2021 08:07:36: Done! pass1 - making usageList (19 chroms): 1 millis pass2 - checking and writing primary data (84 records, 4 fields): 3 millis CompletedMACS2peakCalling