Job ID = 8184457 SRX = SRX8047594 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-08-10T03:23:14 prefetch.2.10.7: 1) Downloading 'SRR11471318'... 2020-08-10T03:23:14 prefetch.2.10.7: Downloading via HTTPS... 2020-08-10T03:24:05 prefetch.2.10.7: HTTPS download succeed 2020-08-10T03:24:06 prefetch.2.10.7: 'SRR11471318' is valid 2020-08-10T03:24:06 prefetch.2.10.7: 1) 'SRR11471318' was downloaded successfully Read 15432207 spots for SRR11471318/SRR11471318.sra Written 15432207 spots for SRR11471318/SRR11471318.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: 00:27:52 15432207 reads; of these: 15432207 (100.00%) were unpaired; of these: 966950 (6.27%) aligned 0 times 8733888 (56.60%) aligned exactly 1 time 5731369 (37.14%) aligned >1 times 93.73% overall alignment rate Time searching: 00:27:56 Overall time: 00:27:56 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] 2611709 / 14465257 = 0.1806 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 12:57:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047594/SRX8047594.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047594/SRX8047594.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047594/SRX8047594.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047594/SRX8047594.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 12:57:01: #1 read tag files... INFO @ Mon, 10 Aug 2020 12:57:01: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 12:57:06: 1000000 INFO @ Mon, 10 Aug 2020 12:57:11: 2000000 INFO @ Mon, 10 Aug 2020 12:57:16: 3000000 INFO @ Mon, 10 Aug 2020 12:57:21: 4000000 INFO @ Mon, 10 Aug 2020 12:57:26: 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 12:57:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047594/SRX8047594.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047594/SRX8047594.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047594/SRX8047594.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047594/SRX8047594.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 12:57:31: #1 read tag files... INFO @ Mon, 10 Aug 2020 12:57:31: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 12:57:31: 6000000 INFO @ Mon, 10 Aug 2020 12:57:36: 7000000 INFO @ Mon, 10 Aug 2020 12:57:36: 1000000 INFO @ Mon, 10 Aug 2020 12:57:41: 8000000 INFO @ Mon, 10 Aug 2020 12:57:42: 2000000 INFO @ Mon, 10 Aug 2020 12:57:46: 9000000 INFO @ Mon, 10 Aug 2020 12:57:48: 3000000 INFO @ Mon, 10 Aug 2020 12:57:51: 10000000 INFO @ Mon, 10 Aug 2020 12:57:54: 4000000 INFO @ Mon, 10 Aug 2020 12:57:56: 11000000 BedGraph に変換中... INFO @ Mon, 10 Aug 2020 12:57:59: 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 12:58:00: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 12:58:00: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 12:58:00: #1 total tags in treatment: 11853548 INFO @ Mon, 10 Aug 2020 12:58:00: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 12:58:00: #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 12:58:01: #1 tags after filtering in treatment: 11853395 INFO @ Mon, 10 Aug 2020 12:58:01: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 12:58:01: #1 finished! INFO @ Mon, 10 Aug 2020 12:58:01: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 12:58:01: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 12:58:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX8047594/SRX8047594.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX8047594/SRX8047594.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX8047594/SRX8047594.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX8047594/SRX8047594.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 12:58:01: #1 read tag files... INFO @ Mon, 10 Aug 2020 12:58:01: #1 read treatment tags... INFO @ Mon, 10 Aug 2020 12:58:02: #2 number of paired peaks: 15695 INFO @ Mon, 10 Aug 2020 12:58:02: start model_add_line... INFO @ Mon, 10 Aug 2020 12:58:02: start X-correlation... INFO @ Mon, 10 Aug 2020 12:58:02: end of X-cor INFO @ Mon, 10 Aug 2020 12:58:02: #2 finished! INFO @ Mon, 10 Aug 2020 12:58:02: #2 predicted fragment length is 53 bps INFO @ Mon, 10 Aug 2020 12:58:02: #2 alternative fragment length(s) may be 53 bps INFO @ Mon, 10 Aug 2020 12:58:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047594/SRX8047594.05_model.r WARNING @ Mon, 10 Aug 2020 12:58:02: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 10 Aug 2020 12:58:02: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Mon, 10 Aug 2020 12:58:02: #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 12:58:02: #3 Call peaks... INFO @ Mon, 10 Aug 2020 12:58:02: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 12:58:05: 6000000 INFO @ Mon, 10 Aug 2020 12:58:07: 1000000 INFO @ Mon, 10 Aug 2020 12:58:10: 7000000 INFO @ Mon, 10 Aug 2020 12:58:13: 2000000 INFO @ Mon, 10 Aug 2020 12:58:16: 8000000 INFO @ Mon, 10 Aug 2020 12:58:19: 3000000 INFO @ Mon, 10 Aug 2020 12:58:21: 9000000 INFO @ Mon, 10 Aug 2020 12:58:24: 4000000 INFO @ Mon, 10 Aug 2020 12:58:27: 10000000 INFO @ Mon, 10 Aug 2020 12:58:28: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 12:58:30: 5000000 INFO @ Mon, 10 Aug 2020 12:58:32: 11000000 INFO @ Mon, 10 Aug 2020 12:58:36: 6000000 INFO @ Mon, 10 Aug 2020 12:58:37: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 12:58:37: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 12:58:37: #1 total tags in treatment: 11853548 INFO @ Mon, 10 Aug 2020 12:58:37: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 12:58:37: #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 12:58:37: #1 tags after filtering in treatment: 11853395 INFO @ Mon, 10 Aug 2020 12:58:37: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 12:58:37: #1 finished! INFO @ Mon, 10 Aug 2020 12:58:37: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 12:58:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 12:58:39: #2 number of paired peaks: 15695 INFO @ Mon, 10 Aug 2020 12:58:39: start model_add_line... INFO @ Mon, 10 Aug 2020 12:58:39: start X-correlation... INFO @ Mon, 10 Aug 2020 12:58:39: end of X-cor INFO @ Mon, 10 Aug 2020 12:58:39: #2 finished! INFO @ Mon, 10 Aug 2020 12:58:39: #2 predicted fragment length is 53 bps INFO @ Mon, 10 Aug 2020 12:58:39: #2 alternative fragment length(s) may be 53 bps INFO @ Mon, 10 Aug 2020 12:58:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047594/SRX8047594.10_model.r WARNING @ Mon, 10 Aug 2020 12:58:39: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 10 Aug 2020 12:58:39: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Mon, 10 Aug 2020 12:58:39: #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 12:58:39: #3 Call peaks... INFO @ Mon, 10 Aug 2020 12:58:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 12:58:41: 7000000 INFO @ Mon, 10 Aug 2020 12:58:42: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047594/SRX8047594.05_peaks.xls INFO @ Mon, 10 Aug 2020 12:58:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047594/SRX8047594.05_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 12:58:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047594/SRX8047594.05_summits.bed INFO @ Mon, 10 Aug 2020 12:58:42: Done! pass1 - making usageList (61 chroms): 2 millis pass2 - checking and writing primary data (3109 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 10 Aug 2020 12:58:47: 8000000 INFO @ Mon, 10 Aug 2020 12:58:52: 9000000 INFO @ Mon, 10 Aug 2020 12:58:58: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 10 Aug 2020 12:59:03: 11000000 INFO @ Mon, 10 Aug 2020 12:59:05: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 12:59:08: #1 tag size is determined as 50 bps INFO @ Mon, 10 Aug 2020 12:59:08: #1 tag size = 50 INFO @ Mon, 10 Aug 2020 12:59:08: #1 total tags in treatment: 11853548 INFO @ Mon, 10 Aug 2020 12:59:08: #1 user defined the maximum tags... INFO @ Mon, 10 Aug 2020 12:59:08: #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 12:59:09: #1 tags after filtering in treatment: 11853395 INFO @ Mon, 10 Aug 2020 12:59:09: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 10 Aug 2020 12:59:09: #1 finished! INFO @ Mon, 10 Aug 2020 12:59:09: #2 Build Peak Model... INFO @ Mon, 10 Aug 2020 12:59:09: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 10 Aug 2020 12:59:10: #2 number of paired peaks: 15695 INFO @ Mon, 10 Aug 2020 12:59:10: start model_add_line... INFO @ Mon, 10 Aug 2020 12:59:10: start X-correlation... INFO @ Mon, 10 Aug 2020 12:59:10: end of X-cor INFO @ Mon, 10 Aug 2020 12:59:10: #2 finished! INFO @ Mon, 10 Aug 2020 12:59:10: #2 predicted fragment length is 53 bps INFO @ Mon, 10 Aug 2020 12:59:10: #2 alternative fragment length(s) may be 53 bps INFO @ Mon, 10 Aug 2020 12:59:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX8047594/SRX8047594.20_model.r WARNING @ Mon, 10 Aug 2020 12:59:10: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 10 Aug 2020 12:59:10: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Mon, 10 Aug 2020 12:59:10: #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 12:59:10: #3 Call peaks... INFO @ Mon, 10 Aug 2020 12:59:10: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 10 Aug 2020 12:59:18: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047594/SRX8047594.10_peaks.xls INFO @ Mon, 10 Aug 2020 12:59:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047594/SRX8047594.10_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 12:59:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047594/SRX8047594.10_summits.bed INFO @ Mon, 10 Aug 2020 12:59:18: Done! pass1 - making usageList (42 chroms): 1 millis pass2 - checking and writing primary data (1159 records, 4 fields): 4 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Mon, 10 Aug 2020 12:59:37: #3 Call peaks for each chromosome... INFO @ Mon, 10 Aug 2020 12:59:51: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX8047594/SRX8047594.20_peaks.xls INFO @ Mon, 10 Aug 2020 12:59:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX8047594/SRX8047594.20_peaks.narrowPeak INFO @ Mon, 10 Aug 2020 12:59:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX8047594/SRX8047594.20_summits.bed INFO @ Mon, 10 Aug 2020 12:59:51: Done! pass1 - making usageList (29 chroms): 1 millis pass2 - checking and writing primary data (467 records, 4 fields): 2 millis CompletedMACS2peakCalling