Job ID = 14518183 SRX = SRX9430850 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 5522670 spots for SRR12979025/SRR12979025.sra Written 5522670 spots for SRR12979025/SRR12979025.sra Read 7020831 spots for SRR12979026/SRR12979026.sra Written 7020831 spots for SRR12979026/SRR12979026.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: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:35:41 12543501 reads; of these: 12543501 (100.00%) were unpaired; of these: 1502090 (11.98%) aligned 0 times 7000058 (55.81%) aligned exactly 1 time 4041353 (32.22%) aligned >1 times 88.02% overall alignment rate Time searching: 00:35:45 Overall time: 00:35:45 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] 2607423 / 11041411 = 0.2361 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 11:27:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX9430850/SRX9430850.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX9430850/SRX9430850.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX9430850/SRX9430850.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX9430850/SRX9430850.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 11:27:56: #1 read tag files... INFO @ Sat, 15 Jan 2022 11:27:56: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 11:28:04: 1000000 INFO @ Sat, 15 Jan 2022 11:28:12: 2000000 INFO @ Sat, 15 Jan 2022 11:28:20: 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 11:28:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX9430850/SRX9430850.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX9430850/SRX9430850.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX9430850/SRX9430850.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX9430850/SRX9430850.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 11:28:25: #1 read tag files... INFO @ Sat, 15 Jan 2022 11:28:25: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 11:28:28: 4000000 INFO @ Sat, 15 Jan 2022 11:28:33: 1000000 INFO @ Sat, 15 Jan 2022 11:28:37: 5000000 INFO @ Sat, 15 Jan 2022 11:28:40: 2000000 INFO @ Sat, 15 Jan 2022 11:28:45: 6000000 INFO @ Sat, 15 Jan 2022 11:28:48: 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 11:28:54: 7000000 INFO @ Sat, 15 Jan 2022 11:28:55: 4000000 INFO @ Sat, 15 Jan 2022 11:28:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX9430850/SRX9430850.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX9430850/SRX9430850.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX9430850/SRX9430850.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX9430850/SRX9430850.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 11:28:56: #1 read tag files... INFO @ Sat, 15 Jan 2022 11:28:56: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 11:29:02: 8000000 INFO @ Sat, 15 Jan 2022 11:29:03: 5000000 INFO @ Sat, 15 Jan 2022 11:29:04: 1000000 INFO @ Sat, 15 Jan 2022 11:29:06: #1 tag size is determined as 60 bps INFO @ Sat, 15 Jan 2022 11:29:06: #1 tag size = 60 INFO @ Sat, 15 Jan 2022 11:29:06: #1 total tags in treatment: 8433988 INFO @ Sat, 15 Jan 2022 11:29:06: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 11:29:06: #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 11:29:07: #1 tags after filtering in treatment: 8433780 INFO @ Sat, 15 Jan 2022 11:29:07: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 11:29:07: #1 finished! INFO @ Sat, 15 Jan 2022 11:29:07: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 11:29:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 11:29:09: #2 number of paired peaks: 24020 INFO @ Sat, 15 Jan 2022 11:29:09: start model_add_line... INFO @ Sat, 15 Jan 2022 11:29:09: start X-correlation... INFO @ Sat, 15 Jan 2022 11:29:09: end of X-cor INFO @ Sat, 15 Jan 2022 11:29:09: #2 finished! INFO @ Sat, 15 Jan 2022 11:29:09: #2 predicted fragment length is 104 bps INFO @ Sat, 15 Jan 2022 11:29:09: #2 alternative fragment length(s) may be 104 bps INFO @ Sat, 15 Jan 2022 11:29:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX9430850/SRX9430850.05_model.r WARNING @ Sat, 15 Jan 2022 11:29:09: #2 Since the d (104) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 11:29:09: #2 You may need to consider one of the other alternative d(s): 104 WARNING @ Sat, 15 Jan 2022 11:29:09: #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 11:29:09: #3 Call peaks... INFO @ Sat, 15 Jan 2022 11:29:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 11:29:10: 6000000 INFO @ Sat, 15 Jan 2022 11:29:13: 2000000 INFO @ Sat, 15 Jan 2022 11:29:18: 7000000 INFO @ Sat, 15 Jan 2022 11:29:21: 3000000 INFO @ Sat, 15 Jan 2022 11:29:26: 8000000 INFO @ Sat, 15 Jan 2022 11:29:26: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 11:29:29: #1 tag size is determined as 60 bps INFO @ Sat, 15 Jan 2022 11:29:29: #1 tag size = 60 INFO @ Sat, 15 Jan 2022 11:29:29: #1 total tags in treatment: 8433988 INFO @ Sat, 15 Jan 2022 11:29:29: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 11:29:29: #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 11:29:30: #1 tags after filtering in treatment: 8433780 INFO @ Sat, 15 Jan 2022 11:29:30: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 11:29:30: #1 finished! INFO @ Sat, 15 Jan 2022 11:29:30: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 11:29:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 11:29:30: 4000000 INFO @ Sat, 15 Jan 2022 11:29:32: #2 number of paired peaks: 24020 INFO @ Sat, 15 Jan 2022 11:29:32: start model_add_line... INFO @ Sat, 15 Jan 2022 11:29:32: start X-correlation... INFO @ Sat, 15 Jan 2022 11:29:32: end of X-cor INFO @ Sat, 15 Jan 2022 11:29:32: #2 finished! INFO @ Sat, 15 Jan 2022 11:29:32: #2 predicted fragment length is 104 bps INFO @ Sat, 15 Jan 2022 11:29:32: #2 alternative fragment length(s) may be 104 bps INFO @ Sat, 15 Jan 2022 11:29:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX9430850/SRX9430850.10_model.r WARNING @ Sat, 15 Jan 2022 11:29:32: #2 Since the d (104) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 11:29:32: #2 You may need to consider one of the other alternative d(s): 104 WARNING @ Sat, 15 Jan 2022 11:29:32: #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 11:29:32: #3 Call peaks... INFO @ Sat, 15 Jan 2022 11:29:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 11:29:36: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX9430850/SRX9430850.05_peaks.xls INFO @ Sat, 15 Jan 2022 11:29:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX9430850/SRX9430850.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 11:29:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX9430850/SRX9430850.05_summits.bed INFO @ Sat, 15 Jan 2022 11:29:37: Done! pass1 - making usageList (73 chroms): 2 millis pass2 - checking and writing primary data (5586 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 11:29:38: 5000000 INFO @ Sat, 15 Jan 2022 11:29:47: 6000000 INFO @ Sat, 15 Jan 2022 11:29:49: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 11:29:55: 7000000 INFO @ Sat, 15 Jan 2022 11:29:59: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX9430850/SRX9430850.10_peaks.xls INFO @ Sat, 15 Jan 2022 11:29:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX9430850/SRX9430850.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 11:29:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX9430850/SRX9430850.10_summits.bed BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 11:29:59: Done! pass1 - making usageList (43 chroms): 1 millis pass2 - checking and writing primary data (1473 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 11:30:03: 8000000 INFO @ Sat, 15 Jan 2022 11:30:07: #1 tag size is determined as 60 bps INFO @ Sat, 15 Jan 2022 11:30:07: #1 tag size = 60 INFO @ Sat, 15 Jan 2022 11:30:07: #1 total tags in treatment: 8433988 INFO @ Sat, 15 Jan 2022 11:30:07: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 11:30:07: #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 11:30:08: #1 tags after filtering in treatment: 8433780 INFO @ Sat, 15 Jan 2022 11:30:08: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 11:30:08: #1 finished! INFO @ Sat, 15 Jan 2022 11:30:08: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 11:30:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 11:30:09: #2 number of paired peaks: 24020 INFO @ Sat, 15 Jan 2022 11:30:09: start model_add_line... INFO @ Sat, 15 Jan 2022 11:30:09: start X-correlation... INFO @ Sat, 15 Jan 2022 11:30:09: end of X-cor INFO @ Sat, 15 Jan 2022 11:30:09: #2 finished! INFO @ Sat, 15 Jan 2022 11:30:09: #2 predicted fragment length is 104 bps INFO @ Sat, 15 Jan 2022 11:30:09: #2 alternative fragment length(s) may be 104 bps INFO @ Sat, 15 Jan 2022 11:30:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX9430850/SRX9430850.20_model.r WARNING @ Sat, 15 Jan 2022 11:30:10: #2 Since the d (104) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 11:30:10: #2 You may need to consider one of the other alternative d(s): 104 WARNING @ Sat, 15 Jan 2022 11:30:10: #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 11:30:10: #3 Call peaks... INFO @ Sat, 15 Jan 2022 11:30:10: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 11:30:27: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 11:30:37: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX9430850/SRX9430850.20_peaks.xls INFO @ Sat, 15 Jan 2022 11:30:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX9430850/SRX9430850.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 11:30:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX9430850/SRX9430850.20_summits.bed INFO @ Sat, 15 Jan 2022 11:30:37: Done! pass1 - making usageList (32 chroms): 1 millis pass2 - checking and writing primary data (449 records, 4 fields): 3 millis CompletedMACS2peakCalling