Job ID = 8184548 SRX = SRX8047606 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-08-10T04:26:54 prefetch.2.10.7: 1) Downloading 'SRR11471330'... 2020-08-10T04:26:54 prefetch.2.10.7: Downloading via HTTPS... 2020-08-10T04:28:12 prefetch.2.10.7: HTTPS download succeed 2020-08-10T04:28:12 prefetch.2.10.7: 1) 'SRR11471330' was downloaded successfully Read 17658861 spots for SRR11471330/SRR11471330.sra Written 17658861 spots for SRR11471330/SRR11471330.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: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:18:00 17658861 reads; of these: 17658861 (100.00%) were unpaired; of these: 4946108 (28.01%) aligned 0 times 9355283 (52.98%) aligned exactly 1 time 3357470 (19.01%) aligned >1 times 71.99% overall alignment rate Time searching: 00:18:02 Overall time: 00:18:02 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] 4512480 / 12712753 = 0.3550 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 @ Mon, 10 Aug 2020 13:50:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047606/SRX8047606.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047606/SRX8047606.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047606/SRX8047606.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047606/SRX8047606.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 @ Mon, 10 Aug 2020 13:50:40: #1 read tag files... INFO @ Mon, 10 Aug 2020 13:50:40: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 13:50:46: 1000000 INFO @ Mon, 10 Aug 2020 13:50:51: 2000000 INFO @ Mon, 10 Aug 2020 13:50:56: 3000000 INFO @ Mon, 10 Aug 2020 13:51:01: 4000000 INFO @ Mon, 10 Aug 2020 13:51:07: 5000000 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 @ Mon, 10 Aug 2020 13:51:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047606/SRX8047606.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047606/SRX8047606.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047606/SRX8047606.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047606/SRX8047606.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 @ Mon, 10 Aug 2020 13:51:10: #1 read tag files... INFO @ Mon, 10 Aug 2020 13:51:10: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 13:51:12: 6000000 INFO @ Mon, 10 Aug 2020 13:51:16: 1000000 INFO @ Mon, 10 Aug 2020 13:51:18: 7000000 INFO @ Mon, 10 Aug 2020 13:51:22: 2000000 INFO @ Mon, 10 Aug 2020 13:51:24: 8000000 INFO @ Mon, 10 Aug 2020 13:51:25: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 13:51:25: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 13:51:25: #1 total tags in treatment: 8200273 INFO @ Mon, 10 Aug 2020 13:51:25: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 13:51:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 10 Aug 2020 13:51:26: #1 tags after filtering in treatment: 8200087 INFO @ Mon, 10 Aug 2020 13:51:26: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 13:51:26: #1 finished! INFO @ Mon, 10 Aug 2020 13:51:26: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 13:51:26: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 13:51:27: #2 number of paired peaks: 22529 INFO @ Mon, 10 Aug 2020 13:51:27: start model_add_line... INFO @ Mon, 10 Aug 2020 13:51:27: start X-correlation... INFO @ Mon, 10 Aug 2020 13:51:27: end of X-cor INFO @ Mon, 10 Aug 2020 13:51:27: #2 finished! INFO @ Mon, 10 Aug 2020 13:51:27: #2 predicted fragment length is 66 bps INFO @ Mon, 10 Aug 2020 13:51:27: #2 alternative fragment length(s) may be 66 bps INFO @ Mon, 10 Aug 2020 13:51:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047606/SRX8047606.05_model.r WARNING @ Mon, 10 Aug 2020 13:51:27: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 10 Aug 2020 13:51:27: #2 You may need to consider one of the other alternative d(s): 66 WARNING @ Mon, 10 Aug 2020 13:51:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 10 Aug 2020 13:51:27: #3 Call peaks... INFO @ Mon, 10 Aug 2020 13:51:27: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 13:51:28: 3000000 INFO @ Mon, 10 Aug 2020 13:51:33: 4000000 INFO @ Mon, 10 Aug 2020 13:51:38: 5000000 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 @ Mon, 10 Aug 2020 13:51:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047606/SRX8047606.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047606/SRX8047606.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047606/SRX8047606.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047606/SRX8047606.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 @ Mon, 10 Aug 2020 13:51:40: #1 read tag files... INFO @ Mon, 10 Aug 2020 13:51:40: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 13:51:44: 6000000 INFO @ Mon, 10 Aug 2020 13:51:45: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 13:51:47: 1000000 INFO @ Mon, 10 Aug 2020 13:51:50: 7000000 INFO @ Mon, 10 Aug 2020 13:51:53: 2000000 INFO @ Mon, 10 Aug 2020 13:51:54: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047606/SRX8047606.05_peaks.xls INFO @ Mon, 10 Aug 2020 13:51:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047606/SRX8047606.05_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 13:51:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047606/SRX8047606.05_summits.bed INFO @ Mon, 10 Aug 2020 13:51:54: Done! pass1 - making usageList (82 chroms): 1 millis pass2 - checking and writing primary data (2102 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 10 Aug 2020 13:51:56: 8000000 INFO @ Mon, 10 Aug 2020 13:51:57: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 13:51:57: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 13:51:57: #1 total tags in treatment: 8200273 INFO @ Mon, 10 Aug 2020 13:51:57: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 13:51:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 10 Aug 2020 13:51:57: #1 tags after filtering in treatment: 8200087 INFO @ Mon, 10 Aug 2020 13:51:57: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 13:51:57: #1 finished! INFO @ Mon, 10 Aug 2020 13:51:57: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 13:51:57: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 13:51:58: 3000000 INFO @ Mon, 10 Aug 2020 13:51:59: #2 number of paired peaks: 22529 INFO @ Mon, 10 Aug 2020 13:51:59: start model_add_line... INFO @ Mon, 10 Aug 2020 13:51:59: start X-correlation... INFO @ Mon, 10 Aug 2020 13:51:59: end of X-cor INFO @ Mon, 10 Aug 2020 13:51:59: #2 finished! INFO @ Mon, 10 Aug 2020 13:51:59: #2 predicted fragment length is 66 bps INFO @ Mon, 10 Aug 2020 13:51:59: #2 alternative fragment length(s) may be 66 bps INFO @ Mon, 10 Aug 2020 13:51:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047606/SRX8047606.10_model.r WARNING @ Mon, 10 Aug 2020 13:51:59: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 10 Aug 2020 13:51:59: #2 You may need to consider one of the other alternative d(s): 66 WARNING @ Mon, 10 Aug 2020 13:51:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 10 Aug 2020 13:51:59: #3 Call peaks... INFO @ Mon, 10 Aug 2020 13:51:59: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 13:52:04: 4000000 INFO @ Mon, 10 Aug 2020 13:52:09: 5000000 INFO @ Mon, 10 Aug 2020 13:52:15: 6000000 INFO @ Mon, 10 Aug 2020 13:52:17: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 13:52:20: 7000000 INFO @ Mon, 10 Aug 2020 13:52:25: 8000000 INFO @ Mon, 10 Aug 2020 13:52:26: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047606/SRX8047606.10_peaks.xls INFO @ Mon, 10 Aug 2020 13:52:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047606/SRX8047606.10_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 13:52:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047606/SRX8047606.10_summits.bed INFO @ Mon, 10 Aug 2020 13:52:26: Done! pass1 - making usageList (60 chroms): 1 millis pass2 - checking and writing primary data (722 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 10 Aug 2020 13:52:27: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 13:52:27: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 13:52:27: #1 total tags in treatment: 8200273 INFO @ Mon, 10 Aug 2020 13:52:27: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 13:52:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 10 Aug 2020 13:52:27: #1 tags after filtering in treatment: 8200087 INFO @ Mon, 10 Aug 2020 13:52:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 13:52:27: #1 finished! INFO @ Mon, 10 Aug 2020 13:52:27: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 13:52:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 13:52:28: #2 number of paired peaks: 22529 INFO @ Mon, 10 Aug 2020 13:52:28: start model_add_line... INFO @ Mon, 10 Aug 2020 13:52:28: start X-correlation... INFO @ Mon, 10 Aug 2020 13:52:28: end of X-cor INFO @ Mon, 10 Aug 2020 13:52:28: #2 finished! INFO @ Mon, 10 Aug 2020 13:52:28: #2 predicted fragment length is 66 bps INFO @ Mon, 10 Aug 2020 13:52:28: #2 alternative fragment length(s) may be 66 bps INFO @ Mon, 10 Aug 2020 13:52:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047606/SRX8047606.20_model.r WARNING @ Mon, 10 Aug 2020 13:52:28: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 10 Aug 2020 13:52:28: #2 You may need to consider one of the other alternative d(s): 66 WARNING @ Mon, 10 Aug 2020 13:52:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 10 Aug 2020 13:52:28: #3 Call peaks... INFO @ Mon, 10 Aug 2020 13:52:28: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 10 Aug 2020 13:52:46: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Mon, 10 Aug 2020 13:52:55: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047606/SRX8047606.20_peaks.xls INFO @ Mon, 10 Aug 2020 13:52:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047606/SRX8047606.20_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 13:52:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047606/SRX8047606.20_summits.bed INFO @ Mon, 10 Aug 2020 13:52:55: Done! pass1 - making usageList (48 chroms): 0 millis pass2 - checking and writing primary data (253 records, 4 fields): 4 millis CompletedMACS2peakCalling