Job ID = 14519599 SRX = SRX6581711 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 24210112 spots for SRR9825044/SRR9825044.sra Written 24210112 spots for SRR9825044/SRR9825044.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: 00:41:47 24210112 reads; of these: 24210112 (100.00%) were unpaired; of these: 709399 (2.93%) aligned 0 times 17105022 (70.65%) aligned exactly 1 time 6395691 (26.42%) aligned >1 times 97.07% overall alignment rate Time searching: 00:41:51 Overall time: 00:41:51 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 12 files... [bam_rmdupse_core] 1694957 / 23500713 = 0.0721 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 17:24:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX6581711/SRX6581711.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX6581711/SRX6581711.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX6581711/SRX6581711.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX6581711/SRX6581711.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 17:24:15: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:24:15: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:24:22: 1000000 INFO @ Sat, 15 Jan 2022 17:24:30: 2000000 INFO @ Sat, 15 Jan 2022 17:24:37: 3000000 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 17:24:44: 4000000 INFO @ Sat, 15 Jan 2022 17:24:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX6581711/SRX6581711.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX6581711/SRX6581711.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX6581711/SRX6581711.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX6581711/SRX6581711.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 17:24:45: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:24:45: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:24:51: 5000000 INFO @ Sat, 15 Jan 2022 17:24:53: 1000000 INFO @ Sat, 15 Jan 2022 17:24:59: 6000000 INFO @ Sat, 15 Jan 2022 17:25:01: 2000000 INFO @ Sat, 15 Jan 2022 17:25:07: 7000000 INFO @ Sat, 15 Jan 2022 17:25:09: 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 17:25:15: 8000000 INFO @ Sat, 15 Jan 2022 17:25:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX6581711/SRX6581711.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX6581711/SRX6581711.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX6581711/SRX6581711.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX6581711/SRX6581711.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 17:25:15: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:25:15: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:25:17: 4000000 INFO @ Sat, 15 Jan 2022 17:25:23: 9000000 INFO @ Sat, 15 Jan 2022 17:25:23: 1000000 INFO @ Sat, 15 Jan 2022 17:25:25: 5000000 INFO @ Sat, 15 Jan 2022 17:25:30: 2000000 INFO @ Sat, 15 Jan 2022 17:25:31: 10000000 INFO @ Sat, 15 Jan 2022 17:25:32: 6000000 INFO @ Sat, 15 Jan 2022 17:25:37: 3000000 INFO @ Sat, 15 Jan 2022 17:25:39: 11000000 INFO @ Sat, 15 Jan 2022 17:25:40: 7000000 INFO @ Sat, 15 Jan 2022 17:25:44: 4000000 INFO @ Sat, 15 Jan 2022 17:25:47: 12000000 INFO @ Sat, 15 Jan 2022 17:25:48: 8000000 INFO @ Sat, 15 Jan 2022 17:25:52: 5000000 INFO @ Sat, 15 Jan 2022 17:25:55: 13000000 INFO @ Sat, 15 Jan 2022 17:25:56: 9000000 INFO @ Sat, 15 Jan 2022 17:25:59: 6000000 INFO @ Sat, 15 Jan 2022 17:26:03: 14000000 INFO @ Sat, 15 Jan 2022 17:26:04: 10000000 INFO @ Sat, 15 Jan 2022 17:26:06: 7000000 INFO @ Sat, 15 Jan 2022 17:26:11: 15000000 INFO @ Sat, 15 Jan 2022 17:26:12: 11000000 INFO @ Sat, 15 Jan 2022 17:26:14: 8000000 INFO @ Sat, 15 Jan 2022 17:26:19: 16000000 INFO @ Sat, 15 Jan 2022 17:26:20: 12000000 INFO @ Sat, 15 Jan 2022 17:26:21: 9000000 INFO @ Sat, 15 Jan 2022 17:26:27: 17000000 INFO @ Sat, 15 Jan 2022 17:26:27: 13000000 INFO @ Sat, 15 Jan 2022 17:26:28: 10000000 INFO @ Sat, 15 Jan 2022 17:26:35: 11000000 INFO @ Sat, 15 Jan 2022 17:26:35: 18000000 INFO @ Sat, 15 Jan 2022 17:26:35: 14000000 INFO @ Sat, 15 Jan 2022 17:26:42: 12000000 INFO @ Sat, 15 Jan 2022 17:26:43: 15000000 INFO @ Sat, 15 Jan 2022 17:26:43: 19000000 INFO @ Sat, 15 Jan 2022 17:26:49: 13000000 INFO @ Sat, 15 Jan 2022 17:26:51: 16000000 INFO @ Sat, 15 Jan 2022 17:26:51: 20000000 INFO @ Sat, 15 Jan 2022 17:26:56: 14000000 INFO @ Sat, 15 Jan 2022 17:26:59: 17000000 INFO @ Sat, 15 Jan 2022 17:27:00: 21000000 INFO @ Sat, 15 Jan 2022 17:27:03: 15000000 INFO @ Sat, 15 Jan 2022 17:27:06: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 17:27:06: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 17:27:06: #1 total tags in treatment: 21805756 INFO @ Sat, 15 Jan 2022 17:27:06: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:27:06: #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 17:27:07: #1 tags after filtering in treatment: 21805629 INFO @ Sat, 15 Jan 2022 17:27:07: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 17:27:07: #1 finished! INFO @ Sat, 15 Jan 2022 17:27:07: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:27:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:27:07: 18000000 INFO @ Sat, 15 Jan 2022 17:27:09: #2 number of paired peaks: 4945 INFO @ Sat, 15 Jan 2022 17:27:09: start model_add_line... INFO @ Sat, 15 Jan 2022 17:27:09: start X-correlation... INFO @ Sat, 15 Jan 2022 17:27:09: end of X-cor INFO @ Sat, 15 Jan 2022 17:27:09: #2 finished! INFO @ Sat, 15 Jan 2022 17:27:09: #2 predicted fragment length is 75 bps INFO @ Sat, 15 Jan 2022 17:27:09: #2 alternative fragment length(s) may be 75 bps INFO @ Sat, 15 Jan 2022 17:27:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX6581711/SRX6581711.05_model.r WARNING @ Sat, 15 Jan 2022 17:27:09: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 17:27:09: #2 You may need to consider one of the other alternative d(s): 75 WARNING @ Sat, 15 Jan 2022 17:27:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 17:27:09: #3 Call peaks... INFO @ Sat, 15 Jan 2022 17:27:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 17:27:10: 16000000 INFO @ Sat, 15 Jan 2022 17:27:14: 19000000 INFO @ Sat, 15 Jan 2022 17:27:17: 17000000 INFO @ Sat, 15 Jan 2022 17:27:21: 20000000 INFO @ Sat, 15 Jan 2022 17:27:24: 18000000 INFO @ Sat, 15 Jan 2022 17:27:29: 21000000 INFO @ Sat, 15 Jan 2022 17:27:31: 19000000 INFO @ Sat, 15 Jan 2022 17:27:35: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 17:27:35: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 17:27:35: #1 total tags in treatment: 21805756 INFO @ Sat, 15 Jan 2022 17:27:35: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:27:35: #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 17:27:36: #1 tags after filtering in treatment: 21805629 INFO @ Sat, 15 Jan 2022 17:27:36: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 17:27:36: #1 finished! INFO @ Sat, 15 Jan 2022 17:27:36: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:27:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:27:38: #2 number of paired peaks: 4945 INFO @ Sat, 15 Jan 2022 17:27:38: start model_add_line... INFO @ Sat, 15 Jan 2022 17:27:38: start X-correlation... INFO @ Sat, 15 Jan 2022 17:27:38: end of X-cor INFO @ Sat, 15 Jan 2022 17:27:38: #2 finished! INFO @ Sat, 15 Jan 2022 17:27:38: #2 predicted fragment length is 75 bps INFO @ Sat, 15 Jan 2022 17:27:38: #2 alternative fragment length(s) may be 75 bps INFO @ Sat, 15 Jan 2022 17:27:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX6581711/SRX6581711.10_model.r WARNING @ Sat, 15 Jan 2022 17:27:38: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 17:27:38: #2 You may need to consider one of the other alternative d(s): 75 WARNING @ Sat, 15 Jan 2022 17:27:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 17:27:38: #3 Call peaks... INFO @ Sat, 15 Jan 2022 17:27:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 17:27:39: 20000000 INFO @ Sat, 15 Jan 2022 17:27:46: 21000000 INFO @ Sat, 15 Jan 2022 17:27:52: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 17:27:52: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 17:27:52: #1 total tags in treatment: 21805756 INFO @ Sat, 15 Jan 2022 17:27:52: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:27:52: #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 17:27:52: #1 tags after filtering in treatment: 21805629 INFO @ Sat, 15 Jan 2022 17:27:52: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 17:27:52: #1 finished! INFO @ Sat, 15 Jan 2022 17:27:52: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:27:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:27:54: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 17:27:54: #2 number of paired peaks: 4945 INFO @ Sat, 15 Jan 2022 17:27:54: start model_add_line... INFO @ Sat, 15 Jan 2022 17:27:54: start X-correlation... INFO @ Sat, 15 Jan 2022 17:27:54: end of X-cor INFO @ Sat, 15 Jan 2022 17:27:54: #2 finished! INFO @ Sat, 15 Jan 2022 17:27:54: #2 predicted fragment length is 75 bps INFO @ Sat, 15 Jan 2022 17:27:54: #2 alternative fragment length(s) may be 75 bps INFO @ Sat, 15 Jan 2022 17:27:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX6581711/SRX6581711.20_model.r WARNING @ Sat, 15 Jan 2022 17:27:54: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 17:27:54: #2 You may need to consider one of the other alternative d(s): 75 WARNING @ Sat, 15 Jan 2022 17:27:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 17:27:54: #3 Call peaks... INFO @ Sat, 15 Jan 2022 17:27:54: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 17:28:20: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX6581711/SRX6581711.05_peaks.xls INFO @ Sat, 15 Jan 2022 17:28:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX6581711/SRX6581711.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 17:28:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX6581711/SRX6581711.05_summits.bed INFO @ Sat, 15 Jan 2022 17:28:20: Done! pass1 - making usageList (50 chroms): 1 millis pass2 - checking and writing primary data (1338 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 17:28:23: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 17:28:39: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 17:28:49: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX6581711/SRX6581711.10_peaks.xls INFO @ Sat, 15 Jan 2022 17:28:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX6581711/SRX6581711.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 17:28:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX6581711/SRX6581711.10_summits.bed INFO @ Sat, 15 Jan 2022 17:28:49: Done! pass1 - making usageList (38 chroms): 1 millis pass2 - checking and writing primary data (777 records, 4 fields): 39 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 17:29:05: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX6581711/SRX6581711.20_peaks.xls INFO @ Sat, 15 Jan 2022 17:29:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX6581711/SRX6581711.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 17:29:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX6581711/SRX6581711.20_summits.bed INFO @ Sat, 15 Jan 2022 17:29:05: Done! pass1 - making usageList (32 chroms): 1 millis pass2 - checking and writing primary data (440 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。