Job ID = 14517869 SRX = SRX6581763 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 17195147 spots for SRR9825037/SRR9825037.sra Written 17195147 spots for SRR9825037/SRR9825037.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: 00:21:32 17195147 reads; of these: 17195147 (100.00%) were unpaired; of these: 424956 (2.47%) aligned 0 times 12442591 (72.36%) aligned exactly 1 time 4327600 (25.17%) aligned >1 times 97.53% overall alignment rate Time searching: 00:21:37 Overall time: 00:21:37 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] 1133130 / 16770191 = 0.0676 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 06:10:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX6581763/SRX6581763.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX6581763/SRX6581763.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX6581763/SRX6581763.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX6581763/SRX6581763.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 06:10:29: #1 read tag files... INFO @ Sat, 15 Jan 2022 06:10:29: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 06:10:38: 1000000 INFO @ Sat, 15 Jan 2022 06:10:44: 2000000 INFO @ Sat, 15 Jan 2022 06:10:52: 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 06:10:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX6581763/SRX6581763.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX6581763/SRX6581763.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX6581763/SRX6581763.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX6581763/SRX6581763.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 06:10:57: #1 read tag files... INFO @ Sat, 15 Jan 2022 06:10:57: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 06:10:59: 4000000 INFO @ Sat, 15 Jan 2022 06:11:05: 1000000 INFO @ Sat, 15 Jan 2022 06:11:06: 5000000 INFO @ Sat, 15 Jan 2022 06:11:13: 2000000 INFO @ Sat, 15 Jan 2022 06:11:13: 6000000 INFO @ Sat, 15 Jan 2022 06:11:20: 7000000 INFO @ Sat, 15 Jan 2022 06:11:22: 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 06:11:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX6581763/SRX6581763.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX6581763/SRX6581763.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX6581763/SRX6581763.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX6581763/SRX6581763.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 06:11:27: #1 read tag files... INFO @ Sat, 15 Jan 2022 06:11:27: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 06:11:27: 8000000 INFO @ Sat, 15 Jan 2022 06:11:30: 4000000 INFO @ Sat, 15 Jan 2022 06:11:34: 1000000 INFO @ Sat, 15 Jan 2022 06:11:35: 9000000 INFO @ Sat, 15 Jan 2022 06:11:39: 5000000 INFO @ Sat, 15 Jan 2022 06:11:41: 2000000 INFO @ Sat, 15 Jan 2022 06:11:41: 10000000 INFO @ Sat, 15 Jan 2022 06:11:45: 6000000 INFO @ Sat, 15 Jan 2022 06:11:48: 3000000 INFO @ Sat, 15 Jan 2022 06:11:50: 11000000 INFO @ Sat, 15 Jan 2022 06:11:52: 7000000 INFO @ Sat, 15 Jan 2022 06:11:56: 4000000 INFO @ Sat, 15 Jan 2022 06:11:57: 12000000 INFO @ Sat, 15 Jan 2022 06:12:00: 8000000 INFO @ Sat, 15 Jan 2022 06:12:03: 5000000 INFO @ Sat, 15 Jan 2022 06:12:05: 13000000 INFO @ Sat, 15 Jan 2022 06:12:08: 9000000 INFO @ Sat, 15 Jan 2022 06:12:09: 6000000 INFO @ Sat, 15 Jan 2022 06:12:13: 14000000 INFO @ Sat, 15 Jan 2022 06:12:16: 7000000 INFO @ Sat, 15 Jan 2022 06:12:17: 10000000 INFO @ Sat, 15 Jan 2022 06:12:21: 15000000 INFO @ Sat, 15 Jan 2022 06:12:24: 8000000 INFO @ Sat, 15 Jan 2022 06:12:25: 11000000 INFO @ Sat, 15 Jan 2022 06:12:26: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 06:12:26: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 06:12:26: #1 total tags in treatment: 15637061 INFO @ Sat, 15 Jan 2022 06:12:26: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 06:12:26: #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 06:12:26: #1 tags after filtering in treatment: 15636886 INFO @ Sat, 15 Jan 2022 06:12:26: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 06:12:26: #1 finished! INFO @ Sat, 15 Jan 2022 06:12:26: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 06:12:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 06:12:28: #2 number of paired peaks: 5095 INFO @ Sat, 15 Jan 2022 06:12:28: start model_add_line... INFO @ Sat, 15 Jan 2022 06:12:28: start X-correlation... INFO @ Sat, 15 Jan 2022 06:12:28: end of X-cor INFO @ Sat, 15 Jan 2022 06:12:28: #2 finished! INFO @ Sat, 15 Jan 2022 06:12:28: #2 predicted fragment length is 75 bps INFO @ Sat, 15 Jan 2022 06:12:28: #2 alternative fragment length(s) may be 75 bps INFO @ Sat, 15 Jan 2022 06:12:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX6581763/SRX6581763.05_model.r WARNING @ Sat, 15 Jan 2022 06:12:28: #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 06:12:28: #2 You may need to consider one of the other alternative d(s): 75 WARNING @ Sat, 15 Jan 2022 06:12:28: #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 06:12:28: #3 Call peaks... INFO @ Sat, 15 Jan 2022 06:12:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 06:12:33: 12000000 INFO @ Sat, 15 Jan 2022 06:12:33: 9000000 INFO @ Sat, 15 Jan 2022 06:12:40: 10000000 INFO @ Sat, 15 Jan 2022 06:12:41: 13000000 INFO @ Sat, 15 Jan 2022 06:12:46: 11000000 INFO @ Sat, 15 Jan 2022 06:12:50: 14000000 INFO @ Sat, 15 Jan 2022 06:12:54: 12000000 INFO @ Sat, 15 Jan 2022 06:12:57: 15000000 INFO @ Sat, 15 Jan 2022 06:13:01: 13000000 INFO @ Sat, 15 Jan 2022 06:13:03: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 06:13:03: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 06:13:03: #1 total tags in treatment: 15637061 INFO @ Sat, 15 Jan 2022 06:13:03: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 06:13:03: #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 06:13:03: #1 tags after filtering in treatment: 15636886 INFO @ Sat, 15 Jan 2022 06:13:03: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 06:13:03: #1 finished! INFO @ Sat, 15 Jan 2022 06:13:03: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 06:13:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 06:13:05: #2 number of paired peaks: 5095 INFO @ Sat, 15 Jan 2022 06:13:05: start model_add_line... INFO @ Sat, 15 Jan 2022 06:13:05: start X-correlation... INFO @ Sat, 15 Jan 2022 06:13:05: end of X-cor INFO @ Sat, 15 Jan 2022 06:13:05: #2 finished! INFO @ Sat, 15 Jan 2022 06:13:05: #2 predicted fragment length is 75 bps INFO @ Sat, 15 Jan 2022 06:13:05: #2 alternative fragment length(s) may be 75 bps INFO @ Sat, 15 Jan 2022 06:13:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX6581763/SRX6581763.10_model.r WARNING @ Sat, 15 Jan 2022 06:13:05: #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 06:13:05: #2 You may need to consider one of the other alternative d(s): 75 WARNING @ Sat, 15 Jan 2022 06:13:05: #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 06:13:05: #3 Call peaks... INFO @ Sat, 15 Jan 2022 06:13:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 06:13:07: 14000000 INFO @ Sat, 15 Jan 2022 06:13:10: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 06:13:14: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 06:13:18: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 06:13:18: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 06:13:18: #1 total tags in treatment: 15637061 INFO @ Sat, 15 Jan 2022 06:13:18: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 06:13:18: #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 06:13:18: #1 tags after filtering in treatment: 15636886 INFO @ Sat, 15 Jan 2022 06:13:18: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 06:13:18: #1 finished! INFO @ Sat, 15 Jan 2022 06:13:18: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 06:13:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 06:13:20: #2 number of paired peaks: 5095 INFO @ Sat, 15 Jan 2022 06:13:20: start model_add_line... INFO @ Sat, 15 Jan 2022 06:13:20: start X-correlation... INFO @ Sat, 15 Jan 2022 06:13:20: end of X-cor INFO @ Sat, 15 Jan 2022 06:13:20: #2 finished! INFO @ Sat, 15 Jan 2022 06:13:20: #2 predicted fragment length is 75 bps INFO @ Sat, 15 Jan 2022 06:13:20: #2 alternative fragment length(s) may be 75 bps INFO @ Sat, 15 Jan 2022 06:13:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX6581763/SRX6581763.20_model.r WARNING @ Sat, 15 Jan 2022 06:13:20: #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 06:13:20: #2 You may need to consider one of the other alternative d(s): 75 WARNING @ Sat, 15 Jan 2022 06:13:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 06:13:20: #3 Call peaks... INFO @ Sat, 15 Jan 2022 06:13:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 06:13:31: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX6581763/SRX6581763.05_peaks.xls INFO @ Sat, 15 Jan 2022 06:13:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX6581763/SRX6581763.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 06:13:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX6581763/SRX6581763.05_summits.bed INFO @ Sat, 15 Jan 2022 06:13:31: Done! pass1 - making usageList (46 chroms): 9 millis pass2 - checking and writing primary data (1025 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 06:13:44: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 06:13:58: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 06:14:04: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX6581763/SRX6581763.10_peaks.xls INFO @ Sat, 15 Jan 2022 06:14:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX6581763/SRX6581763.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 06:14:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX6581763/SRX6581763.10_summits.bed INFO @ Sat, 15 Jan 2022 06:14:04: Done! pass1 - making usageList (35 chroms): 1 millis pass2 - checking and writing primary data (591 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 06:14:19: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX6581763/SRX6581763.20_peaks.xls INFO @ Sat, 15 Jan 2022 06:14:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX6581763/SRX6581763.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 06:14:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX6581763/SRX6581763.20_summits.bed INFO @ Sat, 15 Jan 2022 06:14:19: Done! pass1 - making usageList (25 chroms): 26 millis pass2 - checking and writing primary data (302 records, 4 fields): 24 millis CompletedMACS2peakCalling