Job ID = 7096717 SRX = SRX6922975 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 20149350 spots for SRR10202921/SRR10202921.sra Written 20149350 spots for SRR10202921/SRR10202921.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: 00:00:04 Time loading mirror index: 00:00:02 Multiseed full-index search: 00:23:21 20149350 reads; of these: 20149350 (100.00%) were unpaired; of these: 1046394 (5.19%) aligned 0 times 14536730 (72.14%) aligned exactly 1 time 4566226 (22.66%) aligned >1 times 94.81% overall alignment rate Time searching: 00:23:28 Overall time: 00:23:28 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] 926387 / 19102956 = 0.0485 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Jul 2020 11:33:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX6922975/SRX6922975.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX6922975/SRX6922975.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX6922975/SRX6922975.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX6922975/SRX6922975.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 @ Wed, 22 Jul 2020 11:33:59: #1 read tag files... INFO @ Wed, 22 Jul 2020 11:33:59: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 11:34:06: 1000000 INFO @ Wed, 22 Jul 2020 11:34:13: 2000000 INFO @ Wed, 22 Jul 2020 11:34:20: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Jul 2020 11:34:27: 4000000 INFO @ Wed, 22 Jul 2020 11:34:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX6922975/SRX6922975.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX6922975/SRX6922975.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX6922975/SRX6922975.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX6922975/SRX6922975.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 @ Wed, 22 Jul 2020 11:34:28: #1 read tag files... INFO @ Wed, 22 Jul 2020 11:34:28: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 11:34:34: 5000000 INFO @ Wed, 22 Jul 2020 11:34:36: 1000000 INFO @ Wed, 22 Jul 2020 11:34:41: 6000000 INFO @ Wed, 22 Jul 2020 11:34:44: 2000000 INFO @ Wed, 22 Jul 2020 11:34:49: 7000000 INFO @ Wed, 22 Jul 2020 11:34:51: 3000000 INFO @ Wed, 22 Jul 2020 11:34:56: 8000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 22 Jul 2020 11:34:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX6922975/SRX6922975.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX6922975/SRX6922975.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX6922975/SRX6922975.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX6922975/SRX6922975.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 @ Wed, 22 Jul 2020 11:34:58: #1 read tag files... INFO @ Wed, 22 Jul 2020 11:34:58: #1 read treatment tags... INFO @ Wed, 22 Jul 2020 11:34:59: 4000000 INFO @ Wed, 22 Jul 2020 11:35:04: 9000000 INFO @ Wed, 22 Jul 2020 11:35:06: 1000000 INFO @ Wed, 22 Jul 2020 11:35:07: 5000000 INFO @ Wed, 22 Jul 2020 11:35:11: 10000000 INFO @ Wed, 22 Jul 2020 11:35:14: 2000000 INFO @ Wed, 22 Jul 2020 11:35:15: 6000000 INFO @ Wed, 22 Jul 2020 11:35:19: 11000000 INFO @ Wed, 22 Jul 2020 11:35:21: 3000000 INFO @ Wed, 22 Jul 2020 11:35:23: 7000000 INFO @ Wed, 22 Jul 2020 11:35:27: 12000000 INFO @ Wed, 22 Jul 2020 11:35:29: 4000000 INFO @ Wed, 22 Jul 2020 11:35:30: 8000000 INFO @ Wed, 22 Jul 2020 11:35:35: 13000000 INFO @ Wed, 22 Jul 2020 11:35:37: 5000000 INFO @ Wed, 22 Jul 2020 11:35:38: 9000000 INFO @ Wed, 22 Jul 2020 11:35:42: 14000000 INFO @ Wed, 22 Jul 2020 11:35:44: 6000000 INFO @ Wed, 22 Jul 2020 11:35:45: 10000000 INFO @ Wed, 22 Jul 2020 11:35:50: 15000000 INFO @ Wed, 22 Jul 2020 11:35:52: 7000000 INFO @ Wed, 22 Jul 2020 11:35:53: 11000000 INFO @ Wed, 22 Jul 2020 11:35:58: 16000000 INFO @ Wed, 22 Jul 2020 11:36:00: 8000000 INFO @ Wed, 22 Jul 2020 11:36:01: 12000000 INFO @ Wed, 22 Jul 2020 11:36:06: 17000000 INFO @ Wed, 22 Jul 2020 11:36:07: 9000000 INFO @ Wed, 22 Jul 2020 11:36:08: 13000000 INFO @ Wed, 22 Jul 2020 11:36:14: 18000000 INFO @ Wed, 22 Jul 2020 11:36:15: 10000000 INFO @ Wed, 22 Jul 2020 11:36:15: #1 tag size is determined as 75 bps INFO @ Wed, 22 Jul 2020 11:36:15: #1 tag size = 75 INFO @ Wed, 22 Jul 2020 11:36:15: #1 total tags in treatment: 18176569 INFO @ Wed, 22 Jul 2020 11:36:15: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 11:36:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 11:36:15: #1 tags after filtering in treatment: 18176409 INFO @ Wed, 22 Jul 2020 11:36:15: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Jul 2020 11:36:15: #1 finished! INFO @ Wed, 22 Jul 2020 11:36:15: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 11:36:15: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 11:36:16: 14000000 INFO @ Wed, 22 Jul 2020 11:36:18: #2 number of paired peaks: 29545 INFO @ Wed, 22 Jul 2020 11:36:18: start model_add_line... INFO @ Wed, 22 Jul 2020 11:36:18: start X-correlation... INFO @ Wed, 22 Jul 2020 11:36:18: end of X-cor INFO @ Wed, 22 Jul 2020 11:36:18: #2 finished! INFO @ Wed, 22 Jul 2020 11:36:18: #2 predicted fragment length is 129 bps INFO @ Wed, 22 Jul 2020 11:36:18: #2 alternative fragment length(s) may be 129 bps INFO @ Wed, 22 Jul 2020 11:36:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX6922975/SRX6922975.05_model.r WARNING @ Wed, 22 Jul 2020 11:36:18: #2 Since the d (129) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Jul 2020 11:36:18: #2 You may need to consider one of the other alternative d(s): 129 WARNING @ Wed, 22 Jul 2020 11:36:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Jul 2020 11:36:18: #3 Call peaks... INFO @ Wed, 22 Jul 2020 11:36:18: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 11:36:22: 11000000 INFO @ Wed, 22 Jul 2020 11:36:24: 15000000 INFO @ Wed, 22 Jul 2020 11:36:30: 12000000 INFO @ Wed, 22 Jul 2020 11:36:32: 16000000 INFO @ Wed, 22 Jul 2020 11:36:38: 13000000 INFO @ Wed, 22 Jul 2020 11:36:39: 17000000 INFO @ Wed, 22 Jul 2020 11:36:46: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Jul 2020 11:36:47: 18000000 INFO @ Wed, 22 Jul 2020 11:36:48: #1 tag size is determined as 75 bps INFO @ Wed, 22 Jul 2020 11:36:48: #1 tag size = 75 INFO @ Wed, 22 Jul 2020 11:36:48: #1 total tags in treatment: 18176569 INFO @ Wed, 22 Jul 2020 11:36:48: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 11:36:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 11:36:49: #1 tags after filtering in treatment: 18176409 INFO @ Wed, 22 Jul 2020 11:36:49: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Jul 2020 11:36:49: #1 finished! INFO @ Wed, 22 Jul 2020 11:36:49: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 11:36:49: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 11:36:51: #2 number of paired peaks: 29545 INFO @ Wed, 22 Jul 2020 11:36:51: start model_add_line... INFO @ Wed, 22 Jul 2020 11:36:51: start X-correlation... INFO @ Wed, 22 Jul 2020 11:36:51: end of X-cor INFO @ Wed, 22 Jul 2020 11:36:51: #2 finished! INFO @ Wed, 22 Jul 2020 11:36:51: #2 predicted fragment length is 129 bps INFO @ Wed, 22 Jul 2020 11:36:51: #2 alternative fragment length(s) may be 129 bps INFO @ Wed, 22 Jul 2020 11:36:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX6922975/SRX6922975.10_model.r WARNING @ Wed, 22 Jul 2020 11:36:51: #2 Since the d (129) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Jul 2020 11:36:51: #2 You may need to consider one of the other alternative d(s): 129 WARNING @ Wed, 22 Jul 2020 11:36:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Jul 2020 11:36:51: #3 Call peaks... INFO @ Wed, 22 Jul 2020 11:36:51: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Jul 2020 11:36:53: 15000000 INFO @ Wed, 22 Jul 2020 11:37:00: 16000000 INFO @ Wed, 22 Jul 2020 11:37:01: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 11:37:07: 17000000 INFO @ Wed, 22 Jul 2020 11:37:14: 18000000 INFO @ Wed, 22 Jul 2020 11:37:15: #1 tag size is determined as 75 bps INFO @ Wed, 22 Jul 2020 11:37:15: #1 tag size = 75 INFO @ Wed, 22 Jul 2020 11:37:15: #1 total tags in treatment: 18176569 INFO @ Wed, 22 Jul 2020 11:37:15: #1 user defined the maximum tags... INFO @ Wed, 22 Jul 2020 11:37:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Jul 2020 11:37:16: #1 tags after filtering in treatment: 18176409 INFO @ Wed, 22 Jul 2020 11:37:16: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Jul 2020 11:37:16: #1 finished! INFO @ Wed, 22 Jul 2020 11:37:16: #2 Build Peak Model... INFO @ Wed, 22 Jul 2020 11:37:16: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Jul 2020 11:37:18: #2 number of paired peaks: 29545 INFO @ Wed, 22 Jul 2020 11:37:18: start model_add_line... INFO @ Wed, 22 Jul 2020 11:37:18: start X-correlation... INFO @ Wed, 22 Jul 2020 11:37:18: end of X-cor INFO @ Wed, 22 Jul 2020 11:37:18: #2 finished! INFO @ Wed, 22 Jul 2020 11:37:18: #2 predicted fragment length is 129 bps INFO @ Wed, 22 Jul 2020 11:37:18: #2 alternative fragment length(s) may be 129 bps INFO @ Wed, 22 Jul 2020 11:37:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX6922975/SRX6922975.20_model.r WARNING @ Wed, 22 Jul 2020 11:37:18: #2 Since the d (129) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Jul 2020 11:37:18: #2 You may need to consider one of the other alternative d(s): 129 WARNING @ Wed, 22 Jul 2020 11:37:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Jul 2020 11:37:18: #3 Call peaks... INFO @ Wed, 22 Jul 2020 11:37:18: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Wed, 22 Jul 2020 11:37:25: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX6922975/SRX6922975.05_peaks.xls INFO @ Wed, 22 Jul 2020 11:37:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX6922975/SRX6922975.05_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 11:37:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX6922975/SRX6922975.05_summits.bed INFO @ Wed, 22 Jul 2020 11:37:25: Done! pass1 - making usageList (103 chroms): 5 millis pass2 - checking and writing primary data (27960 records, 4 fields): 39 millis CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 11:37:35: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 11:37:59: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX6922975/SRX6922975.10_peaks.xls INFO @ Wed, 22 Jul 2020 11:37:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX6922975/SRX6922975.10_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 11:37:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX6922975/SRX6922975.10_summits.bed INFO @ Wed, 22 Jul 2020 11:37:59: Done! pass1 - making usageList (77 chroms): 5 millis pass2 - checking and writing primary data (21380 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Wed, 22 Jul 2020 11:38:01: #3 Call peaks for each chromosome... INFO @ Wed, 22 Jul 2020 11:38:25: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX6922975/SRX6922975.20_peaks.xls INFO @ Wed, 22 Jul 2020 11:38:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX6922975/SRX6922975.20_peaks.narrowPeak INFO @ Wed, 22 Jul 2020 11:38:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX6922975/SRX6922975.20_summits.bed INFO @ Wed, 22 Jul 2020 11:38:25: Done! pass1 - making usageList (47 chroms): 3 millis pass2 - checking and writing primary data (13142 records, 4 fields): 30 millis CompletedMACS2peakCalling