Job ID = 14519606 SRX = SRX6581718 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 15753829 spots for SRR9825051/SRR9825051.sra Written 15753829 spots for SRR9825051/SRR9825051.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: 00:23:52 15753829 reads; of these: 15753829 (100.00%) were unpaired; of these: 440880 (2.80%) aligned 0 times 11142433 (70.73%) aligned exactly 1 time 4170516 (26.47%) aligned >1 times 97.20% overall alignment rate Time searching: 00:23:57 Overall time: 00:23:57 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] 1088795 / 15312949 = 0.0711 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 17:07:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX6581718/SRX6581718.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX6581718/SRX6581718.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX6581718/SRX6581718.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX6581718/SRX6581718.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 17:07:31: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:07:31: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:07:37: 1000000 INFO @ Sat, 15 Jan 2022 17:07:42: 2000000 INFO @ Sat, 15 Jan 2022 17:07:48: 3000000 INFO @ Sat, 15 Jan 2022 17:07:53: 4000000 INFO @ Sat, 15 Jan 2022 17:07:58: 5000000 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 17:08:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX6581718/SRX6581718.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX6581718/SRX6581718.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX6581718/SRX6581718.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX6581718/SRX6581718.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 17:08:01: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:08:01: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:08:04: 6000000 INFO @ Sat, 15 Jan 2022 17:08:07: 1000000 INFO @ Sat, 15 Jan 2022 17:08:10: 7000000 INFO @ Sat, 15 Jan 2022 17:08:12: 2000000 INFO @ Sat, 15 Jan 2022 17:08:15: 8000000 INFO @ Sat, 15 Jan 2022 17:08:18: 3000000 INFO @ Sat, 15 Jan 2022 17:08:21: 9000000 INFO @ Sat, 15 Jan 2022 17:08:24: 4000000 INFO @ Sat, 15 Jan 2022 17:08:26: 10000000 BedGraph に変換中... INFO @ Sat, 15 Jan 2022 17:08:29: 5000000 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 17:08:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX6581718/SRX6581718.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX6581718/SRX6581718.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX6581718/SRX6581718.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX6581718/SRX6581718.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 17:08:31: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:08:31: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:08:32: 11000000 INFO @ Sat, 15 Jan 2022 17:08:35: 6000000 INFO @ Sat, 15 Jan 2022 17:08:37: 1000000 INFO @ Sat, 15 Jan 2022 17:08:38: 12000000 INFO @ Sat, 15 Jan 2022 17:08:41: 7000000 INFO @ Sat, 15 Jan 2022 17:08:44: 13000000 INFO @ Sat, 15 Jan 2022 17:08:44: 2000000 INFO @ Sat, 15 Jan 2022 17:08:46: 8000000 INFO @ Sat, 15 Jan 2022 17:08:50: 14000000 INFO @ Sat, 15 Jan 2022 17:08:50: 3000000 INFO @ Sat, 15 Jan 2022 17:08:51: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 17:08:51: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 17:08:51: #1 total tags in treatment: 14224154 INFO @ Sat, 15 Jan 2022 17:08:51: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:08:51: #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 17:08:51: #1 tags after filtering in treatment: 14223974 INFO @ Sat, 15 Jan 2022 17:08:51: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 17:08:51: #1 finished! INFO @ Sat, 15 Jan 2022 17:08:51: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:08:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:08:52: 9000000 INFO @ Sat, 15 Jan 2022 17:08:53: #2 number of paired peaks: 4797 INFO @ Sat, 15 Jan 2022 17:08:53: start model_add_line... INFO @ Sat, 15 Jan 2022 17:08:53: start X-correlation... INFO @ Sat, 15 Jan 2022 17:08:53: end of X-cor INFO @ Sat, 15 Jan 2022 17:08:53: #2 finished! INFO @ Sat, 15 Jan 2022 17:08:53: #2 predicted fragment length is 74 bps INFO @ Sat, 15 Jan 2022 17:08:53: #2 alternative fragment length(s) may be 74 bps INFO @ Sat, 15 Jan 2022 17:08:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX6581718/SRX6581718.05_model.r WARNING @ Sat, 15 Jan 2022 17:08:53: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 17:08:53: #2 You may need to consider one of the other alternative d(s): 74 WARNING @ Sat, 15 Jan 2022 17:08:53: #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 17:08:53: #3 Call peaks... INFO @ Sat, 15 Jan 2022 17:08:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 17:08:57: 4000000 INFO @ Sat, 15 Jan 2022 17:08:58: 10000000 INFO @ Sat, 15 Jan 2022 17:09:03: 5000000 INFO @ Sat, 15 Jan 2022 17:09:04: 11000000 INFO @ Sat, 15 Jan 2022 17:09:09: 12000000 INFO @ Sat, 15 Jan 2022 17:09:10: 6000000 INFO @ Sat, 15 Jan 2022 17:09:15: 13000000 INFO @ Sat, 15 Jan 2022 17:09:16: 7000000 INFO @ Sat, 15 Jan 2022 17:09:21: 14000000 INFO @ Sat, 15 Jan 2022 17:09:22: 8000000 INFO @ Sat, 15 Jan 2022 17:09:22: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 17:09:22: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 17:09:22: #1 total tags in treatment: 14224154 INFO @ Sat, 15 Jan 2022 17:09:22: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:09:22: #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 17:09:23: #1 tags after filtering in treatment: 14223974 INFO @ Sat, 15 Jan 2022 17:09:23: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 17:09:23: #1 finished! INFO @ Sat, 15 Jan 2022 17:09:23: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:09:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:09:24: #2 number of paired peaks: 4797 INFO @ Sat, 15 Jan 2022 17:09:24: start model_add_line... INFO @ Sat, 15 Jan 2022 17:09:24: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 17:09:24: start X-correlation... INFO @ Sat, 15 Jan 2022 17:09:24: end of X-cor INFO @ Sat, 15 Jan 2022 17:09:24: #2 finished! INFO @ Sat, 15 Jan 2022 17:09:24: #2 predicted fragment length is 74 bps INFO @ Sat, 15 Jan 2022 17:09:24: #2 alternative fragment length(s) may be 74 bps INFO @ Sat, 15 Jan 2022 17:09:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX6581718/SRX6581718.10_model.r WARNING @ Sat, 15 Jan 2022 17:09:24: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 17:09:24: #2 You may need to consider one of the other alternative d(s): 74 WARNING @ Sat, 15 Jan 2022 17:09:24: #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 17:09:24: #3 Call peaks... INFO @ Sat, 15 Jan 2022 17:09:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 17:09:29: 9000000 INFO @ Sat, 15 Jan 2022 17:09:35: 10000000 INFO @ Sat, 15 Jan 2022 17:09:40: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX6581718/SRX6581718.05_peaks.xls INFO @ Sat, 15 Jan 2022 17:09:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX6581718/SRX6581718.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 17:09:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX6581718/SRX6581718.05_summits.bed INFO @ Sat, 15 Jan 2022 17:09:40: Done! pass1 - making usageList (46 chroms): 1 millis pass2 - checking and writing primary data (995 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 17:09:41: 11000000 INFO @ Sat, 15 Jan 2022 17:09:47: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 17:09:53: 13000000 INFO @ Sat, 15 Jan 2022 17:09:56: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 17:10:00: 14000000 INFO @ Sat, 15 Jan 2022 17:10:01: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 17:10:01: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 17:10:01: #1 total tags in treatment: 14224154 INFO @ Sat, 15 Jan 2022 17:10:01: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:10:01: #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 17:10:01: #1 tags after filtering in treatment: 14223974 INFO @ Sat, 15 Jan 2022 17:10:01: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 17:10:01: #1 finished! INFO @ Sat, 15 Jan 2022 17:10:01: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:10:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:10:03: #2 number of paired peaks: 4797 INFO @ Sat, 15 Jan 2022 17:10:03: start model_add_line... INFO @ Sat, 15 Jan 2022 17:10:03: start X-correlation... INFO @ Sat, 15 Jan 2022 17:10:03: end of X-cor INFO @ Sat, 15 Jan 2022 17:10:03: #2 finished! INFO @ Sat, 15 Jan 2022 17:10:03: #2 predicted fragment length is 74 bps INFO @ Sat, 15 Jan 2022 17:10:03: #2 alternative fragment length(s) may be 74 bps INFO @ Sat, 15 Jan 2022 17:10:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX6581718/SRX6581718.20_model.r WARNING @ Sat, 15 Jan 2022 17:10:03: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 17:10:03: #2 You may need to consider one of the other alternative d(s): 74 WARNING @ Sat, 15 Jan 2022 17:10:03: #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 17:10:03: #3 Call peaks... INFO @ Sat, 15 Jan 2022 17:10:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 17:10:11: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX6581718/SRX6581718.10_peaks.xls INFO @ Sat, 15 Jan 2022 17:10:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX6581718/SRX6581718.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 17:10:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX6581718/SRX6581718.10_summits.bed INFO @ Sat, 15 Jan 2022 17:10:11: Done! pass1 - making usageList (36 chroms): 0 millis pass2 - checking and writing primary data (601 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 17:10:35: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 17:10:50: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX6581718/SRX6581718.20_peaks.xls INFO @ Sat, 15 Jan 2022 17:10:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX6581718/SRX6581718.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 17:10:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX6581718/SRX6581718.20_summits.bed INFO @ Sat, 15 Jan 2022 17:10:50: Done! pass1 - making usageList (28 chroms): 1 millis pass2 - checking and writing primary data (342 records, 4 fields): 14 millis CompletedMACS2peakCalling