Job ID = 14517867 SRX = SRX6581761 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 12836229 spots for SRR9825035/SRR9825035.sra Written 12836229 spots for SRR9825035/SRR9825035.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:16:26 12836229 reads; of these: 12836229 (100.00%) were unpaired; of these: 308558 (2.40%) aligned 0 times 9231955 (71.92%) aligned exactly 1 time 3295716 (25.68%) aligned >1 times 97.60% overall alignment rate Time searching: 00:16:27 Overall time: 00:16:27 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 8 files... [bam_rmdupse_core] 770515 / 12527671 = 0.0615 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 05:58:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX6581761/SRX6581761.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX6581761/SRX6581761.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX6581761/SRX6581761.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX6581761/SRX6581761.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 05:58:29: #1 read tag files... INFO @ Sat, 15 Jan 2022 05:58:29: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 05:58:37: 1000000 INFO @ Sat, 15 Jan 2022 05:58:45: 2000000 INFO @ Sat, 15 Jan 2022 05:58:52: 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 05:58:59: 4000000 INFO @ Sat, 15 Jan 2022 05:58:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX6581761/SRX6581761.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX6581761/SRX6581761.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX6581761/SRX6581761.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX6581761/SRX6581761.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 05:58:59: #1 read tag files... INFO @ Sat, 15 Jan 2022 05:58:59: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 05:59:06: 5000000 INFO @ Sat, 15 Jan 2022 05:59:07: 1000000 INFO @ Sat, 15 Jan 2022 05:59:14: 6000000 INFO @ Sat, 15 Jan 2022 05:59:15: 2000000 INFO @ Sat, 15 Jan 2022 05:59:22: 7000000 INFO @ Sat, 15 Jan 2022 05:59:23: 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 05:59:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX6581761/SRX6581761.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX6581761/SRX6581761.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX6581761/SRX6581761.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX6581761/SRX6581761.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 05:59:29: #1 read tag files... INFO @ Sat, 15 Jan 2022 05:59:29: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 05:59:30: 8000000 INFO @ Sat, 15 Jan 2022 05:59:30: 4000000 INFO @ Sat, 15 Jan 2022 05:59:37: 1000000 INFO @ Sat, 15 Jan 2022 05:59:38: 9000000 INFO @ Sat, 15 Jan 2022 05:59:38: 5000000 INFO @ Sat, 15 Jan 2022 05:59:45: 2000000 INFO @ Sat, 15 Jan 2022 05:59:46: 10000000 INFO @ Sat, 15 Jan 2022 05:59:46: 6000000 INFO @ Sat, 15 Jan 2022 05:59:53: 3000000 INFO @ Sat, 15 Jan 2022 05:59:54: 11000000 INFO @ Sat, 15 Jan 2022 05:59:54: 7000000 INFO @ Sat, 15 Jan 2022 06:00:00: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 06:00:00: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 06:00:00: #1 total tags in treatment: 11757156 INFO @ Sat, 15 Jan 2022 06:00:00: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 06:00:00: #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 06:00:00: #1 tags after filtering in treatment: 11756970 INFO @ Sat, 15 Jan 2022 06:00:00: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 06:00:00: #1 finished! INFO @ Sat, 15 Jan 2022 06:00:00: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 06:00:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 06:00:01: 4000000 INFO @ Sat, 15 Jan 2022 06:00:01: #2 number of paired peaks: 5338 INFO @ Sat, 15 Jan 2022 06:00:01: start model_add_line... INFO @ Sat, 15 Jan 2022 06:00:01: start X-correlation... INFO @ Sat, 15 Jan 2022 06:00:01: end of X-cor INFO @ Sat, 15 Jan 2022 06:00:01: #2 finished! INFO @ Sat, 15 Jan 2022 06:00:01: #2 predicted fragment length is 75 bps INFO @ Sat, 15 Jan 2022 06:00:01: #2 alternative fragment length(s) may be 75 bps INFO @ Sat, 15 Jan 2022 06:00:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX6581761/SRX6581761.05_model.r WARNING @ Sat, 15 Jan 2022 06:00:01: #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 06:00:01: #2 You may need to consider one of the other alternative d(s): 75 WARNING @ Sat, 15 Jan 2022 06:00:01: #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 06:00:01: #3 Call peaks... INFO @ Sat, 15 Jan 2022 06:00:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 06:00:02: 8000000 INFO @ Sat, 15 Jan 2022 06:00:08: 5000000 INFO @ Sat, 15 Jan 2022 06:00:09: 9000000 INFO @ Sat, 15 Jan 2022 06:00:16: 6000000 INFO @ Sat, 15 Jan 2022 06:00:16: 10000000 INFO @ Sat, 15 Jan 2022 06:00:23: 7000000 INFO @ Sat, 15 Jan 2022 06:00:23: 11000000 INFO @ Sat, 15 Jan 2022 06:00:27: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 06:00:29: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 06:00:29: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 06:00:29: #1 total tags in treatment: 11757156 INFO @ Sat, 15 Jan 2022 06:00:29: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 06:00:29: #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 06:00:29: #1 tags after filtering in treatment: 11756970 INFO @ Sat, 15 Jan 2022 06:00:29: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 06:00:29: #1 finished! INFO @ Sat, 15 Jan 2022 06:00:29: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 06:00:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 06:00:30: 8000000 INFO @ Sat, 15 Jan 2022 06:00:30: #2 number of paired peaks: 5338 INFO @ Sat, 15 Jan 2022 06:00:30: start model_add_line... INFO @ Sat, 15 Jan 2022 06:00:30: start X-correlation... INFO @ Sat, 15 Jan 2022 06:00:30: end of X-cor INFO @ Sat, 15 Jan 2022 06:00:30: #2 finished! INFO @ Sat, 15 Jan 2022 06:00:30: #2 predicted fragment length is 75 bps INFO @ Sat, 15 Jan 2022 06:00:30: #2 alternative fragment length(s) may be 75 bps INFO @ Sat, 15 Jan 2022 06:00:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX6581761/SRX6581761.10_model.r WARNING @ Sat, 15 Jan 2022 06:00:30: #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 06:00:30: #2 You may need to consider one of the other alternative d(s): 75 WARNING @ Sat, 15 Jan 2022 06:00:30: #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 06:00:30: #3 Call peaks... INFO @ Sat, 15 Jan 2022 06:00:30: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 06:00:36: 9000000 INFO @ Sat, 15 Jan 2022 06:00:40: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX6581761/SRX6581761.05_peaks.xls INFO @ Sat, 15 Jan 2022 06:00:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX6581761/SRX6581761.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 06:00:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX6581761/SRX6581761.05_summits.bed INFO @ Sat, 15 Jan 2022 06:00:40: Done! pass1 - making usageList (42 chroms): 1 millis pass2 - checking and writing primary data (814 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 06:00:43: 10000000 INFO @ Sat, 15 Jan 2022 06:00:49: 11000000 INFO @ Sat, 15 Jan 2022 06:00:54: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 06:00:54: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 06:00:54: #1 total tags in treatment: 11757156 INFO @ Sat, 15 Jan 2022 06:00:54: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 06:00:54: #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 06:00:54: #1 tags after filtering in treatment: 11756970 INFO @ Sat, 15 Jan 2022 06:00:54: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 06:00:54: #1 finished! INFO @ Sat, 15 Jan 2022 06:00:54: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 06:00:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 06:00:55: #2 number of paired peaks: 5338 INFO @ Sat, 15 Jan 2022 06:00:55: start model_add_line... INFO @ Sat, 15 Jan 2022 06:00:56: start X-correlation... INFO @ Sat, 15 Jan 2022 06:00:56: end of X-cor INFO @ Sat, 15 Jan 2022 06:00:56: #2 finished! INFO @ Sat, 15 Jan 2022 06:00:56: #2 predicted fragment length is 75 bps INFO @ Sat, 15 Jan 2022 06:00:56: #2 alternative fragment length(s) may be 75 bps INFO @ Sat, 15 Jan 2022 06:00:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX6581761/SRX6581761.20_model.r WARNING @ Sat, 15 Jan 2022 06:00:56: #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 06:00:56: #2 You may need to consider one of the other alternative d(s): 75 WARNING @ Sat, 15 Jan 2022 06:00:56: #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 06:00:56: #3 Call peaks... INFO @ Sat, 15 Jan 2022 06:00:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 06:00:57: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 06:01:10: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX6581761/SRX6581761.10_peaks.xls INFO @ Sat, 15 Jan 2022 06:01:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX6581761/SRX6581761.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 06:01:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX6581761/SRX6581761.10_summits.bed INFO @ Sat, 15 Jan 2022 06:01:10: Done! pass1 - making usageList (33 chroms): 0 millis pass2 - checking and writing primary data (488 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 06:01:22: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 06:01:35: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX6581761/SRX6581761.20_peaks.xls INFO @ Sat, 15 Jan 2022 06:01:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX6581761/SRX6581761.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 06:01:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX6581761/SRX6581761.20_summits.bed INFO @ Sat, 15 Jan 2022 06:01:35: Done! pass1 - making usageList (23 chroms): 1 millis pass2 - checking and writing primary data (253 records, 4 fields): 2 millis CompletedMACS2peakCalling