Job ID = 14519609 SRX = SRX6581721 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 17086341 spots for SRR9825054/SRR9825054.sra Written 17086341 spots for SRR9825054/SRR9825054.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: 00:20:54 17086341 reads; of these: 17086341 (100.00%) were unpaired; of these: 423117 (2.48%) aligned 0 times 12242431 (71.65%) aligned exactly 1 time 4420793 (25.87%) aligned >1 times 97.52% overall alignment rate Time searching: 00:20:57 Overall time: 00:20:57 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] 1499564 / 16663224 = 0.0900 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 17:07:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX6581721/SRX6581721.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX6581721/SRX6581721.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX6581721/SRX6581721.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX6581721/SRX6581721.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 17:07:27: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:07:27: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:07:34: 1000000 INFO @ Sat, 15 Jan 2022 17:07:40: 2000000 INFO @ Sat, 15 Jan 2022 17:07:47: 3000000 INFO @ Sat, 15 Jan 2022 17:07:53: 4000000 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 17:07:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX6581721/SRX6581721.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX6581721/SRX6581721.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX6581721/SRX6581721.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX6581721/SRX6581721.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 17:07:57: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:07:57: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:08:00: 5000000 INFO @ Sat, 15 Jan 2022 17:08:05: 1000000 INFO @ Sat, 15 Jan 2022 17:08:09: 6000000 INFO @ Sat, 15 Jan 2022 17:08:14: 2000000 INFO @ Sat, 15 Jan 2022 17:08:17: 7000000 INFO @ Sat, 15 Jan 2022 17:08:22: 3000000 INFO @ Sat, 15 Jan 2022 17:08:25: 8000000 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 17:08:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX6581721/SRX6581721.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX6581721/SRX6581721.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX6581721/SRX6581721.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX6581721/SRX6581721.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 17:08:27: #1 read tag files... INFO @ Sat, 15 Jan 2022 17:08:27: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 17:08:30: 4000000 INFO @ Sat, 15 Jan 2022 17:08:33: 9000000 INFO @ Sat, 15 Jan 2022 17:08:36: 1000000 INFO @ Sat, 15 Jan 2022 17:08:38: 5000000 INFO @ Sat, 15 Jan 2022 17:08:41: 10000000 INFO @ Sat, 15 Jan 2022 17:08:44: 2000000 INFO @ Sat, 15 Jan 2022 17:08:46: 6000000 INFO @ Sat, 15 Jan 2022 17:08:50: 11000000 INFO @ Sat, 15 Jan 2022 17:08:52: 3000000 INFO @ Sat, 15 Jan 2022 17:08:54: 7000000 INFO @ Sat, 15 Jan 2022 17:08:58: 12000000 INFO @ Sat, 15 Jan 2022 17:09:00: 4000000 INFO @ Sat, 15 Jan 2022 17:09:02: 8000000 INFO @ Sat, 15 Jan 2022 17:09:06: 13000000 INFO @ Sat, 15 Jan 2022 17:09:08: 5000000 INFO @ Sat, 15 Jan 2022 17:09:10: 9000000 INFO @ Sat, 15 Jan 2022 17:09:14: 14000000 INFO @ Sat, 15 Jan 2022 17:09:17: 6000000 INFO @ Sat, 15 Jan 2022 17:09:18: 10000000 INFO @ Sat, 15 Jan 2022 17:09:22: 15000000 INFO @ Sat, 15 Jan 2022 17:09:24: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 17:09:24: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 17:09:24: #1 total tags in treatment: 15163660 INFO @ Sat, 15 Jan 2022 17:09:24: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:09:24: #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 17:09:24: #1 tags after filtering in treatment: 15163503 INFO @ Sat, 15 Jan 2022 17:09:24: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 17:09:24: #1 finished! INFO @ Sat, 15 Jan 2022 17:09:24: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:09:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:09:25: 7000000 INFO @ Sat, 15 Jan 2022 17:09:25: #2 number of paired peaks: 4551 INFO @ Sat, 15 Jan 2022 17:09:25: start model_add_line... INFO @ Sat, 15 Jan 2022 17:09:25: start X-correlation... INFO @ Sat, 15 Jan 2022 17:09:26: end of X-cor INFO @ Sat, 15 Jan 2022 17:09:26: #2 finished! INFO @ Sat, 15 Jan 2022 17:09:26: #2 predicted fragment length is 75 bps INFO @ Sat, 15 Jan 2022 17:09:26: #2 alternative fragment length(s) may be 75 bps INFO @ Sat, 15 Jan 2022 17:09:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX6581721/SRX6581721.05_model.r WARNING @ Sat, 15 Jan 2022 17:09:26: #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 17:09:26: #2 You may need to consider one of the other alternative d(s): 75 WARNING @ Sat, 15 Jan 2022 17:09:26: #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 17:09:26: #3 Call peaks... INFO @ Sat, 15 Jan 2022 17:09:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 17:09:26: 11000000 INFO @ Sat, 15 Jan 2022 17:09:33: 8000000 INFO @ Sat, 15 Jan 2022 17:09:34: 12000000 INFO @ Sat, 15 Jan 2022 17:09:41: 9000000 INFO @ Sat, 15 Jan 2022 17:09:41: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 17:09:49: 10000000 INFO @ Sat, 15 Jan 2022 17:09:49: 14000000 INFO @ Sat, 15 Jan 2022 17:09:57: 11000000 INFO @ Sat, 15 Jan 2022 17:09:58: 15000000 INFO @ Sat, 15 Jan 2022 17:09:58: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 17:09:59: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 17:09:59: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 17:09:59: #1 total tags in treatment: 15163660 INFO @ Sat, 15 Jan 2022 17:09:59: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:09:59: #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 17:09:59: #1 tags after filtering in treatment: 15163503 INFO @ Sat, 15 Jan 2022 17:09:59: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 17:09:59: #1 finished! INFO @ Sat, 15 Jan 2022 17:09:59: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:09:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:10:01: #2 number of paired peaks: 4551 INFO @ Sat, 15 Jan 2022 17:10:01: start model_add_line... INFO @ Sat, 15 Jan 2022 17:10:01: start X-correlation... INFO @ Sat, 15 Jan 2022 17:10:01: end of X-cor INFO @ Sat, 15 Jan 2022 17:10:01: #2 finished! INFO @ Sat, 15 Jan 2022 17:10:01: #2 predicted fragment length is 75 bps INFO @ Sat, 15 Jan 2022 17:10:01: #2 alternative fragment length(s) may be 75 bps INFO @ Sat, 15 Jan 2022 17:10:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX6581721/SRX6581721.10_model.r WARNING @ Sat, 15 Jan 2022 17:10:01: #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 17:10:01: #2 You may need to consider one of the other alternative d(s): 75 WARNING @ Sat, 15 Jan 2022 17:10:01: #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 17:10:01: #3 Call peaks... INFO @ Sat, 15 Jan 2022 17:10:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 17:10:04: 12000000 INFO @ Sat, 15 Jan 2022 17:10:11: 13000000 INFO @ Sat, 15 Jan 2022 17:10:14: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX6581721/SRX6581721.05_peaks.xls INFO @ Sat, 15 Jan 2022 17:10:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX6581721/SRX6581721.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 17:10:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX6581721/SRX6581721.05_summits.bed INFO @ Sat, 15 Jan 2022 17:10:14: Done! pass1 - making usageList (43 chroms): 1 millis pass2 - checking and writing primary data (971 records, 4 fields): 4 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 17:10:18: 14000000 INFO @ Sat, 15 Jan 2022 17:10:25: 15000000 INFO @ Sat, 15 Jan 2022 17:10:26: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 17:10:26: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 17:10:26: #1 total tags in treatment: 15163660 INFO @ Sat, 15 Jan 2022 17:10:26: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 17:10:26: #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 17:10:27: #1 tags after filtering in treatment: 15163503 INFO @ Sat, 15 Jan 2022 17:10:27: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 17:10:27: #1 finished! INFO @ Sat, 15 Jan 2022 17:10:27: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 17:10:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 17:10:28: #2 number of paired peaks: 4551 INFO @ Sat, 15 Jan 2022 17:10:28: start model_add_line... INFO @ Sat, 15 Jan 2022 17:10:28: start X-correlation... INFO @ Sat, 15 Jan 2022 17:10:28: end of X-cor INFO @ Sat, 15 Jan 2022 17:10:28: #2 finished! INFO @ Sat, 15 Jan 2022 17:10:28: #2 predicted fragment length is 75 bps INFO @ Sat, 15 Jan 2022 17:10:28: #2 alternative fragment length(s) may be 75 bps INFO @ Sat, 15 Jan 2022 17:10:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX6581721/SRX6581721.20_model.r WARNING @ Sat, 15 Jan 2022 17:10:28: #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 17:10:28: #2 You may need to consider one of the other alternative d(s): 75 WARNING @ Sat, 15 Jan 2022 17:10:28: #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 17:10:28: #3 Call peaks... INFO @ Sat, 15 Jan 2022 17:10:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 17:10:35: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 17:10:51: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX6581721/SRX6581721.10_peaks.xls INFO @ Sat, 15 Jan 2022 17:10:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX6581721/SRX6581721.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 17:10:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX6581721/SRX6581721.10_summits.bed INFO @ Sat, 15 Jan 2022 17:10:51: Done! pass1 - making usageList (34 chroms): 0 millis pass2 - checking and writing primary data (591 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 17:11:01: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 17:11:18: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX6581721/SRX6581721.20_peaks.xls INFO @ Sat, 15 Jan 2022 17:11:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX6581721/SRX6581721.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 17:11:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX6581721/SRX6581721.20_summits.bed INFO @ Sat, 15 Jan 2022 17:11:18: Done! pass1 - making usageList (25 chroms): 1 millis pass2 - checking and writing primary data (327 records, 4 fields): 2 millis CompletedMACS2peakCalling