Job ID = 12531440 SRX = SRX3087665 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 109334228 spots for SRR6445104/SRR6445104.sra Written 109334228 spots for SRR6445104/SRR6445104.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: 01:51:22 109334228 reads; of these: 109334228 (100.00%) were unpaired; of these: 22588740 (20.66%) aligned 0 times 63038960 (57.66%) aligned exactly 1 time 23706528 (21.68%) aligned >1 times 79.34% overall alignment rate Time searching: 01:51:27 Overall time: 01:51:27 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 36 files... [bam_rmdupse_core] 62966885 / 86745488 = 0.7259 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 09:46:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX3087665/SRX3087665.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX3087665/SRX3087665.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX3087665/SRX3087665.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX3087665/SRX3087665.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 09:46:33: #1 read tag files... INFO @ Sat, 17 Apr 2021 09:46:33: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 09:46:46: 1000000 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 09:47:01: 2000000 INFO @ Sat, 17 Apr 2021 09:47:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX3087665/SRX3087665.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX3087665/SRX3087665.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX3087665/SRX3087665.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX3087665/SRX3087665.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 09:47:03: #1 read tag files... INFO @ Sat, 17 Apr 2021 09:47:03: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 09:47:11: 1000000 INFO @ Sat, 17 Apr 2021 09:47:15: 3000000 INFO @ Sat, 17 Apr 2021 09:47:19: 2000000 INFO @ Sat, 17 Apr 2021 09:47:27: 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 09:47:30: 4000000 INFO @ Sat, 17 Apr 2021 09:47:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX3087665/SRX3087665.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX3087665/SRX3087665.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX3087665/SRX3087665.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX3087665/SRX3087665.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 09:47:33: #1 read tag files... INFO @ Sat, 17 Apr 2021 09:47:33: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 09:47:36: 4000000 INFO @ Sat, 17 Apr 2021 09:47:44: 1000000 INFO @ Sat, 17 Apr 2021 09:47:44: 5000000 INFO @ Sat, 17 Apr 2021 09:47:45: 5000000 INFO @ Sat, 17 Apr 2021 09:47:54: 6000000 INFO @ Sat, 17 Apr 2021 09:47:56: 2000000 INFO @ Sat, 17 Apr 2021 09:47:58: 6000000 INFO @ Sat, 17 Apr 2021 09:48:03: 7000000 INFO @ Sat, 17 Apr 2021 09:48:07: 3000000 INFO @ Sat, 17 Apr 2021 09:48:11: 7000000 INFO @ Sat, 17 Apr 2021 09:48:11: 8000000 INFO @ Sat, 17 Apr 2021 09:48:18: 4000000 INFO @ Sat, 17 Apr 2021 09:48:20: 9000000 INFO @ Sat, 17 Apr 2021 09:48:28: 8000000 INFO @ Sat, 17 Apr 2021 09:48:29: 10000000 INFO @ Sat, 17 Apr 2021 09:48:31: 5000000 INFO @ Sat, 17 Apr 2021 09:48:37: 11000000 INFO @ Sat, 17 Apr 2021 09:48:43: 9000000 INFO @ Sat, 17 Apr 2021 09:48:44: 6000000 INFO @ Sat, 17 Apr 2021 09:48:46: 12000000 INFO @ Sat, 17 Apr 2021 09:48:55: 13000000 INFO @ Sat, 17 Apr 2021 09:48:58: 7000000 INFO @ Sat, 17 Apr 2021 09:48:58: 10000000 INFO @ Sat, 17 Apr 2021 09:49:03: 14000000 INFO @ Sat, 17 Apr 2021 09:49:12: 15000000 INFO @ Sat, 17 Apr 2021 09:49:12: 11000000 INFO @ Sat, 17 Apr 2021 09:49:13: 8000000 INFO @ Sat, 17 Apr 2021 09:49:21: 16000000 INFO @ Sat, 17 Apr 2021 09:49:26: 12000000 INFO @ Sat, 17 Apr 2021 09:49:30: 17000000 INFO @ Sat, 17 Apr 2021 09:49:31: 9000000 INFO @ Sat, 17 Apr 2021 09:49:38: 18000000 INFO @ Sat, 17 Apr 2021 09:49:40: 13000000 INFO @ Sat, 17 Apr 2021 09:49:47: 10000000 INFO @ Sat, 17 Apr 2021 09:49:47: 19000000 INFO @ Sat, 17 Apr 2021 09:49:56: 20000000 INFO @ Sat, 17 Apr 2021 09:49:56: 14000000 INFO @ Sat, 17 Apr 2021 09:50:03: 11000000 INFO @ Sat, 17 Apr 2021 09:50:05: 21000000 INFO @ Sat, 17 Apr 2021 09:50:11: 15000000 INFO @ Sat, 17 Apr 2021 09:50:13: 22000000 INFO @ Sat, 17 Apr 2021 09:50:15: 12000000 INFO @ Sat, 17 Apr 2021 09:50:22: 23000000 INFO @ Sat, 17 Apr 2021 09:50:26: 16000000 INFO @ Sat, 17 Apr 2021 09:50:29: #1 tag size is determined as 61 bps INFO @ Sat, 17 Apr 2021 09:50:29: #1 tag size = 61 INFO @ Sat, 17 Apr 2021 09:50:29: #1 total tags in treatment: 23778603 INFO @ Sat, 17 Apr 2021 09:50:29: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 09:50:29: #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 09:50:30: #1 tags after filtering in treatment: 23778508 INFO @ Sat, 17 Apr 2021 09:50:30: 13000000 INFO @ Sat, 17 Apr 2021 09:50:30: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 17 Apr 2021 09:50:30: #1 finished! INFO @ Sat, 17 Apr 2021 09:50:30: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 09:50:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 09:50:33: #2 number of paired peaks: 32207 INFO @ Sat, 17 Apr 2021 09:50:33: start model_add_line... INFO @ Sat, 17 Apr 2021 09:50:33: start X-correlation... INFO @ Sat, 17 Apr 2021 09:50:33: end of X-cor INFO @ Sat, 17 Apr 2021 09:50:33: #2 finished! INFO @ Sat, 17 Apr 2021 09:50:33: #2 predicted fragment length is 95 bps INFO @ Sat, 17 Apr 2021 09:50:33: #2 alternative fragment length(s) may be 95 bps INFO @ Sat, 17 Apr 2021 09:50:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX3087665/SRX3087665.10_model.r WARNING @ Sat, 17 Apr 2021 09:50:33: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 09:50:33: #2 You may need to consider one of the other alternative d(s): 95 WARNING @ Sat, 17 Apr 2021 09:50:33: #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 09:50:33: #3 Call peaks... INFO @ Sat, 17 Apr 2021 09:50:33: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 17 Apr 2021 09:50:41: 17000000 INFO @ Sat, 17 Apr 2021 09:50:46: 14000000 INFO @ Sat, 17 Apr 2021 09:50:58: 18000000 INFO @ Sat, 17 Apr 2021 09:51:00: 15000000 INFO @ Sat, 17 Apr 2021 09:51:15: 19000000 INFO @ Sat, 17 Apr 2021 09:51:16: 16000000 INFO @ Sat, 17 Apr 2021 09:51:27: 20000000 INFO @ Sat, 17 Apr 2021 09:51:33: 17000000 BigWig に変換しました。 INFO @ Sat, 17 Apr 2021 09:51:39: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 09:51:40: 21000000 INFO @ Sat, 17 Apr 2021 09:51:49: 18000000 INFO @ Sat, 17 Apr 2021 09:51:53: 22000000 INFO @ Sat, 17 Apr 2021 09:52:04: 19000000 INFO @ Sat, 17 Apr 2021 09:52:07: 23000000 INFO @ Sat, 17 Apr 2021 09:52:12: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX3087665/SRX3087665.10_peaks.xls INFO @ Sat, 17 Apr 2021 09:52:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX3087665/SRX3087665.10_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 09:52:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX3087665/SRX3087665.10_summits.bed INFO @ Sat, 17 Apr 2021 09:52:12: Done! pass1 - making usageList (77 chroms): 4 millis pass2 - checking and writing primary data (12426 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sat, 17 Apr 2021 09:52:16: #1 tag size is determined as 61 bps INFO @ Sat, 17 Apr 2021 09:52:16: #1 tag size = 61 INFO @ Sat, 17 Apr 2021 09:52:16: #1 total tags in treatment: 23778603 INFO @ Sat, 17 Apr 2021 09:52:16: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 09:52:16: #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 09:52:17: #1 tags after filtering in treatment: 23778508 INFO @ Sat, 17 Apr 2021 09:52:17: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 17 Apr 2021 09:52:17: #1 finished! INFO @ Sat, 17 Apr 2021 09:52:17: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 09:52:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 09:52:20: 20000000 INFO @ Sat, 17 Apr 2021 09:52:21: #2 number of paired peaks: 32207 INFO @ Sat, 17 Apr 2021 09:52:21: start model_add_line... INFO @ Sat, 17 Apr 2021 09:52:21: start X-correlation... INFO @ Sat, 17 Apr 2021 09:52:21: end of X-cor INFO @ Sat, 17 Apr 2021 09:52:21: #2 finished! INFO @ Sat, 17 Apr 2021 09:52:21: #2 predicted fragment length is 95 bps INFO @ Sat, 17 Apr 2021 09:52:21: #2 alternative fragment length(s) may be 95 bps INFO @ Sat, 17 Apr 2021 09:52:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX3087665/SRX3087665.05_model.r WARNING @ Sat, 17 Apr 2021 09:52:21: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 09:52:21: #2 You may need to consider one of the other alternative d(s): 95 WARNING @ Sat, 17 Apr 2021 09:52:21: #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 09:52:21: #3 Call peaks... INFO @ Sat, 17 Apr 2021 09:52:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 09:52:33: 21000000 INFO @ Sat, 17 Apr 2021 09:52:46: 22000000 INFO @ Sat, 17 Apr 2021 09:53:00: 23000000 INFO @ Sat, 17 Apr 2021 09:53:12: #1 tag size is determined as 61 bps INFO @ Sat, 17 Apr 2021 09:53:12: #1 tag size = 61 INFO @ Sat, 17 Apr 2021 09:53:12: #1 total tags in treatment: 23778603 INFO @ Sat, 17 Apr 2021 09:53:12: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 09:53:12: #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 09:53:13: #1 tags after filtering in treatment: 23778508 INFO @ Sat, 17 Apr 2021 09:53:13: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 17 Apr 2021 09:53:13: #1 finished! INFO @ Sat, 17 Apr 2021 09:53:13: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 09:53:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 09:53:17: #2 number of paired peaks: 32207 INFO @ Sat, 17 Apr 2021 09:53:17: start model_add_line... INFO @ Sat, 17 Apr 2021 09:53:17: start X-correlation... INFO @ Sat, 17 Apr 2021 09:53:17: end of X-cor INFO @ Sat, 17 Apr 2021 09:53:17: #2 finished! INFO @ Sat, 17 Apr 2021 09:53:17: #2 predicted fragment length is 95 bps INFO @ Sat, 17 Apr 2021 09:53:17: #2 alternative fragment length(s) may be 95 bps INFO @ Sat, 17 Apr 2021 09:53:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX3087665/SRX3087665.20_model.r WARNING @ Sat, 17 Apr 2021 09:53:17: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 09:53:17: #2 You may need to consider one of the other alternative d(s): 95 WARNING @ Sat, 17 Apr 2021 09:53:17: #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 09:53:17: #3 Call peaks... INFO @ Sat, 17 Apr 2021 09:53:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 09:53:43: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 09:54:29: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX3087665/SRX3087665.05_peaks.xls INFO @ Sat, 17 Apr 2021 09:54:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX3087665/SRX3087665.05_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 09:54:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX3087665/SRX3087665.05_summits.bed INFO @ Sat, 17 Apr 2021 09:54:29: Done! pass1 - making usageList (115 chroms): 6 millis pass2 - checking and writing primary data (24382 records, 4 fields): 39 millis CompletedMACS2peakCalling INFO @ Sat, 17 Apr 2021 09:54:43: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 09:55:26: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX3087665/SRX3087665.20_peaks.xls INFO @ Sat, 17 Apr 2021 09:55:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX3087665/SRX3087665.20_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 09:55:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX3087665/SRX3087665.20_summits.bed INFO @ Sat, 17 Apr 2021 09:55:27: Done! pass1 - making usageList (47 chroms): 2 millis pass2 - checking and writing primary data (3967 records, 4 fields): 12 millis CompletedMACS2peakCalling