Job ID = 12531435 SRX = SRX3087662 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 89599987 spots for SRR5927298/SRR5927298.sra Written 89599987 spots for SRR5927298/SRR5927298.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: 01:05:00 89599987 reads; of these: 89599987 (100.00%) were unpaired; of these: 31595808 (35.26%) aligned 0 times 40877516 (45.62%) aligned exactly 1 time 17126663 (19.11%) aligned >1 times 64.74% overall alignment rate Time searching: 01:05:05 Overall time: 01:05:05 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 24 files... [bam_rmdupse_core] 41697289 / 58004179 = 0.7189 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 08:45:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX3087662/SRX3087662.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX3087662/SRX3087662.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX3087662/SRX3087662.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX3087662/SRX3087662.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 08:45:08: #1 read tag files... INFO @ Sat, 17 Apr 2021 08:45:08: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 08:45:16: 1000000 INFO @ Sat, 17 Apr 2021 08:45:24: 2000000 INFO @ Sat, 17 Apr 2021 08:45:32: 3000000 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 08:45:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX3087662/SRX3087662.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX3087662/SRX3087662.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX3087662/SRX3087662.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX3087662/SRX3087662.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 08:45:38: #1 read tag files... INFO @ Sat, 17 Apr 2021 08:45:38: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 08:45:40: 4000000 INFO @ Sat, 17 Apr 2021 08:45:47: 1000000 INFO @ Sat, 17 Apr 2021 08:45:49: 5000000 INFO @ Sat, 17 Apr 2021 08:45:56: 2000000 INFO @ Sat, 17 Apr 2021 08:45:58: 6000000 INFO @ Sat, 17 Apr 2021 08:46:05: 3000000 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 08:46:07: 7000000 INFO @ Sat, 17 Apr 2021 08:46:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX3087662/SRX3087662.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX3087662/SRX3087662.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX3087662/SRX3087662.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX3087662/SRX3087662.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 08:46:08: #1 read tag files... INFO @ Sat, 17 Apr 2021 08:46:08: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 08:46:14: 4000000 INFO @ Sat, 17 Apr 2021 08:46:15: 8000000 INFO @ Sat, 17 Apr 2021 08:46:18: 1000000 INFO @ Sat, 17 Apr 2021 08:46:23: 5000000 INFO @ Sat, 17 Apr 2021 08:46:24: 9000000 INFO @ Sat, 17 Apr 2021 08:46:27: 2000000 INFO @ Sat, 17 Apr 2021 08:46:32: 6000000 INFO @ Sat, 17 Apr 2021 08:46:33: 10000000 INFO @ Sat, 17 Apr 2021 08:46:37: 3000000 INFO @ Sat, 17 Apr 2021 08:46:41: 7000000 INFO @ Sat, 17 Apr 2021 08:46:42: 11000000 INFO @ Sat, 17 Apr 2021 08:46:46: 4000000 INFO @ Sat, 17 Apr 2021 08:46:50: 8000000 INFO @ Sat, 17 Apr 2021 08:46:50: 12000000 INFO @ Sat, 17 Apr 2021 08:46:55: 5000000 INFO @ Sat, 17 Apr 2021 08:46:59: 9000000 INFO @ Sat, 17 Apr 2021 08:46:59: 13000000 INFO @ Sat, 17 Apr 2021 08:47:04: 6000000 INFO @ Sat, 17 Apr 2021 08:47:08: 10000000 INFO @ Sat, 17 Apr 2021 08:47:08: 14000000 INFO @ Sat, 17 Apr 2021 08:47:13: 7000000 INFO @ Sat, 17 Apr 2021 08:47:17: 11000000 INFO @ Sat, 17 Apr 2021 08:47:17: 15000000 INFO @ Sat, 17 Apr 2021 08:47:22: 8000000 INFO @ Sat, 17 Apr 2021 08:47:26: 12000000 INFO @ Sat, 17 Apr 2021 08:47:27: 16000000 INFO @ Sat, 17 Apr 2021 08:47:30: #1 tag size is determined as 61 bps INFO @ Sat, 17 Apr 2021 08:47:30: #1 tag size = 61 INFO @ Sat, 17 Apr 2021 08:47:30: #1 total tags in treatment: 16306890 INFO @ Sat, 17 Apr 2021 08:47:30: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 08:47:30: #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 08:47:30: #1 tags after filtering in treatment: 16306771 INFO @ Sat, 17 Apr 2021 08:47:30: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 17 Apr 2021 08:47:30: #1 finished! INFO @ Sat, 17 Apr 2021 08:47:30: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 08:47:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 08:47:31: 9000000 INFO @ Sat, 17 Apr 2021 08:47:32: #2 number of paired peaks: 16625 INFO @ Sat, 17 Apr 2021 08:47:32: start model_add_line... INFO @ Sat, 17 Apr 2021 08:47:33: start X-correlation... INFO @ Sat, 17 Apr 2021 08:47:33: end of X-cor INFO @ Sat, 17 Apr 2021 08:47:33: #2 finished! INFO @ Sat, 17 Apr 2021 08:47:33: #2 predicted fragment length is 62 bps INFO @ Sat, 17 Apr 2021 08:47:33: #2 alternative fragment length(s) may be 62 bps INFO @ Sat, 17 Apr 2021 08:47:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX3087662/SRX3087662.05_model.r WARNING @ Sat, 17 Apr 2021 08:47:33: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 08:47:33: #2 You may need to consider one of the other alternative d(s): 62 WARNING @ Sat, 17 Apr 2021 08:47:33: #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 08:47:33: #3 Call peaks... INFO @ Sat, 17 Apr 2021 08:47:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 08:47:35: 13000000 INFO @ Sat, 17 Apr 2021 08:47:40: 10000000 INFO @ Sat, 17 Apr 2021 08:47:44: 14000000 INFO @ Sat, 17 Apr 2021 08:47:49: 11000000 INFO @ Sat, 17 Apr 2021 08:47:53: 15000000 INFO @ Sat, 17 Apr 2021 08:47:58: 12000000 INFO @ Sat, 17 Apr 2021 08:48:02: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 17 Apr 2021 08:48:04: #1 tag size is determined as 61 bps INFO @ Sat, 17 Apr 2021 08:48:04: #1 tag size = 61 INFO @ Sat, 17 Apr 2021 08:48:04: #1 total tags in treatment: 16306890 INFO @ Sat, 17 Apr 2021 08:48:04: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 08:48:04: #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 08:48:05: #1 tags after filtering in treatment: 16306771 INFO @ Sat, 17 Apr 2021 08:48:05: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 17 Apr 2021 08:48:05: #1 finished! INFO @ Sat, 17 Apr 2021 08:48:05: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 08:48:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 08:48:07: 13000000 INFO @ Sat, 17 Apr 2021 08:48:07: #2 number of paired peaks: 16625 INFO @ Sat, 17 Apr 2021 08:48:07: start model_add_line... INFO @ Sat, 17 Apr 2021 08:48:07: start X-correlation... INFO @ Sat, 17 Apr 2021 08:48:07: end of X-cor INFO @ Sat, 17 Apr 2021 08:48:07: #2 finished! INFO @ Sat, 17 Apr 2021 08:48:07: #2 predicted fragment length is 62 bps INFO @ Sat, 17 Apr 2021 08:48:07: #2 alternative fragment length(s) may be 62 bps INFO @ Sat, 17 Apr 2021 08:48:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX3087662/SRX3087662.10_model.r WARNING @ Sat, 17 Apr 2021 08:48:07: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 08:48:07: #2 You may need to consider one of the other alternative d(s): 62 WARNING @ Sat, 17 Apr 2021 08:48:07: #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 08:48:07: #3 Call peaks... INFO @ Sat, 17 Apr 2021 08:48:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 08:48:14: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 08:48:15: 14000000 INFO @ Sat, 17 Apr 2021 08:48:23: 15000000 INFO @ Sat, 17 Apr 2021 08:48:31: 16000000 INFO @ Sat, 17 Apr 2021 08:48:34: #1 tag size is determined as 61 bps INFO @ Sat, 17 Apr 2021 08:48:34: #1 tag size = 61 INFO @ Sat, 17 Apr 2021 08:48:34: #1 total tags in treatment: 16306890 INFO @ Sat, 17 Apr 2021 08:48:34: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 08:48:34: #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 08:48:34: #1 tags after filtering in treatment: 16306771 INFO @ Sat, 17 Apr 2021 08:48:34: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 17 Apr 2021 08:48:34: #1 finished! INFO @ Sat, 17 Apr 2021 08:48:34: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 08:48:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 08:48:36: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX3087662/SRX3087662.05_peaks.xls INFO @ Sat, 17 Apr 2021 08:48:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX3087662/SRX3087662.05_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 08:48:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX3087662/SRX3087662.05_summits.bed INFO @ Sat, 17 Apr 2021 08:48:36: Done! INFO @ Sat, 17 Apr 2021 08:48:36: #2 number of paired peaks: 16625 INFO @ Sat, 17 Apr 2021 08:48:36: start model_add_line... pass1 - making usageList (44 chroms): 0 millis pass2 - checking and writing primary data (1407 records, 4 fields): 8 millis INFO @ Sat, 17 Apr 2021 08:48:37: start X-correlation... CompletedMACS2peakCalling INFO @ Sat, 17 Apr 2021 08:48:37: end of X-cor INFO @ Sat, 17 Apr 2021 08:48:37: #2 finished! INFO @ Sat, 17 Apr 2021 08:48:37: #2 predicted fragment length is 62 bps INFO @ Sat, 17 Apr 2021 08:48:37: #2 alternative fragment length(s) may be 62 bps INFO @ Sat, 17 Apr 2021 08:48:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX3087662/SRX3087662.20_model.r WARNING @ Sat, 17 Apr 2021 08:48:37: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 08:48:37: #2 You may need to consider one of the other alternative d(s): 62 WARNING @ Sat, 17 Apr 2021 08:48:37: #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 08:48:37: #3 Call peaks... INFO @ Sat, 17 Apr 2021 08:48:37: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 17 Apr 2021 08:48:51: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 08:49:13: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX3087662/SRX3087662.10_peaks.xls INFO @ Sat, 17 Apr 2021 08:49:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX3087662/SRX3087662.10_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 08:49:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX3087662/SRX3087662.10_summits.bed INFO @ Sat, 17 Apr 2021 08:49:13: Done! pass1 - making usageList (36 chroms): 1 millis pass2 - checking and writing primary data (715 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 17 Apr 2021 08:49:20: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 08:49:43: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX3087662/SRX3087662.20_peaks.xls INFO @ Sat, 17 Apr 2021 08:49:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX3087662/SRX3087662.20_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 08:49:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX3087662/SRX3087662.20_summits.bed INFO @ Sat, 17 Apr 2021 08:49:43: Done! pass1 - making usageList (27 chroms): 1 millis pass2 - checking and writing primary data (290 records, 4 fields): 2 millis CompletedMACS2peakCalling