Job ID = 6453469 SRX = SRX1166568 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:18:32 prefetch.2.10.7: 1) Downloading 'SRR2189004'... 2020-06-21T08:18:32 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:21:20 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:21:20 prefetch.2.10.7: 'SRR2189004' is valid 2020-06-21T08:21:20 prefetch.2.10.7: 1) 'SRR2189004' was downloaded successfully 2020-06-21T08:22:12 prefetch.2.10.7: 'SRR2189004' has 10 unresolved dependencies 2020-06-21T08:22:12 prefetch.2.10.7: 2) Downloading 'ncbi-acc:NC_004353.3?vdb-ctx=refseq'... 2020-06-21T08:22:12 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:22:25 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:22:25 prefetch.2.10.7: 2) 'ncbi-acc:NC_004353.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T08:22:25 prefetch.2.10.7: 3) Downloading 'ncbi-acc:NC_004354.3?vdb-ctx=refseq'... 2020-06-21T08:22:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:22:42 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:22:42 prefetch.2.10.7: 3) 'ncbi-acc:NC_004354.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T08:22:42 prefetch.2.10.7: 4) Downloading 'ncbi-acc:NS_000188.1?vdb-ctx=refseq'... 2020-06-21T08:22:42 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:22:58 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:22:58 prefetch.2.10.7: 4) 'ncbi-acc:NS_000188.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T08:22:58 prefetch.2.10.7: 5) Downloading 'ncbi-acc:NT_033777.2?vdb-ctx=refseq'... 2020-06-21T08:22:58 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:23:20 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:23:20 prefetch.2.10.7: 5) 'ncbi-acc:NT_033777.2?vdb-ctx=refseq' was downloaded successfully 2020-06-21T08:23:20 prefetch.2.10.7: 6) Downloading 'ncbi-acc:NT_033778.3?vdb-ctx=refseq'... 2020-06-21T08:23:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:23:37 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:23:37 prefetch.2.10.7: 6) 'ncbi-acc:NT_033778.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T08:23:37 prefetch.2.10.7: 7) Downloading 'ncbi-acc:NT_033779.4?vdb-ctx=refseq'... 2020-06-21T08:23:37 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:23:54 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:23:54 prefetch.2.10.7: 7) 'ncbi-acc:NT_033779.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T08:23:54 prefetch.2.10.7: 8) Downloading 'ncbi-acc:NT_037436.3?vdb-ctx=refseq'... 2020-06-21T08:23:54 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:24:14 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:24:14 prefetch.2.10.7: 8) 'ncbi-acc:NT_037436.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T08:24:14 prefetch.2.10.7: 9) Downloading 'ncbi-acc:NW_001848856.1?vdb-ctx=refseq'... 2020-06-21T08:24:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:24:27 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:24:27 prefetch.2.10.7: 9) 'ncbi-acc:NW_001848856.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T08:24:27 prefetch.2.10.7: 10) Downloading 'ncbi-acc:NW_001848857.1?vdb-ctx=refseq'... 2020-06-21T08:24:27 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:24:39 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:24:39 prefetch.2.10.7: 10) 'ncbi-acc:NW_001848857.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T08:24:39 prefetch.2.10.7: 11) Downloading 'ncbi-acc:NW_001848858.1?vdb-ctx=refseq'... 2020-06-21T08:24:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:24:53 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:24:53 prefetch.2.10.7: 11) 'ncbi-acc:NW_001848858.1?vdb-ctx=refseq' was downloaded successfully Read 28669362 spots for SRR2189004/SRR2189004.sra Written 28669362 spots for SRR2189004/SRR2189004.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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:25 28669362 reads; of these: 28669362 (100.00%) were unpaired; of these: 646501 (2.26%) aligned 0 times 22074512 (77.00%) aligned exactly 1 time 5948349 (20.75%) aligned >1 times 97.74% overall alignment rate Time searching: 00:06:25 Overall time: 00:06:25 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 12863261 / 28022861 = 0.4590 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 @ Sun, 21 Jun 2020 17:38:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1166568/SRX1166568.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1166568/SRX1166568.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1166568/SRX1166568.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1166568/SRX1166568.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 17:38:04: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:38:04: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:38:10: 1000000 INFO @ Sun, 21 Jun 2020 17:38:16: 2000000 INFO @ Sun, 21 Jun 2020 17:38:23: 3000000 INFO @ Sun, 21 Jun 2020 17:38:29: 4000000 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 @ Sun, 21 Jun 2020 17:38:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1166568/SRX1166568.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1166568/SRX1166568.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1166568/SRX1166568.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1166568/SRX1166568.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 17:38:34: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:38:34: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:38:35: 5000000 INFO @ Sun, 21 Jun 2020 17:38:40: 1000000 INFO @ Sun, 21 Jun 2020 17:38:42: 6000000 INFO @ Sun, 21 Jun 2020 17:38:47: 2000000 INFO @ Sun, 21 Jun 2020 17:38:49: 7000000 INFO @ Sun, 21 Jun 2020 17:38:54: 3000000 INFO @ Sun, 21 Jun 2020 17:38:56: 8000000 INFO @ Sun, 21 Jun 2020 17:39:00: 4000000 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 @ Sun, 21 Jun 2020 17:39:03: 9000000 INFO @ Sun, 21 Jun 2020 17:39:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1166568/SRX1166568.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1166568/SRX1166568.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1166568/SRX1166568.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1166568/SRX1166568.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 17:39:04: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:39:04: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:39:07: 5000000 INFO @ Sun, 21 Jun 2020 17:39:10: 10000000 INFO @ Sun, 21 Jun 2020 17:39:11: 1000000 INFO @ Sun, 21 Jun 2020 17:39:14: 6000000 INFO @ Sun, 21 Jun 2020 17:39:16: 11000000 INFO @ Sun, 21 Jun 2020 17:39:17: 2000000 INFO @ Sun, 21 Jun 2020 17:39:21: 7000000 INFO @ Sun, 21 Jun 2020 17:39:24: 12000000 INFO @ Sun, 21 Jun 2020 17:39:24: 3000000 INFO @ Sun, 21 Jun 2020 17:39:28: 8000000 INFO @ Sun, 21 Jun 2020 17:39:30: 13000000 INFO @ Sun, 21 Jun 2020 17:39:31: 4000000 INFO @ Sun, 21 Jun 2020 17:39:35: 9000000 INFO @ Sun, 21 Jun 2020 17:39:37: 14000000 INFO @ Sun, 21 Jun 2020 17:39:38: 5000000 INFO @ Sun, 21 Jun 2020 17:39:42: 10000000 INFO @ Sun, 21 Jun 2020 17:39:45: 15000000 INFO @ Sun, 21 Jun 2020 17:39:45: 6000000 INFO @ Sun, 21 Jun 2020 17:39:46: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:39:46: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:39:46: #1 total tags in treatment: 15159600 INFO @ Sun, 21 Jun 2020 17:39:46: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:39:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 17:39:46: #1 tags after filtering in treatment: 15159538 INFO @ Sun, 21 Jun 2020 17:39:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:39:46: #1 finished! INFO @ Sun, 21 Jun 2020 17:39:46: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:39:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:39:47: #2 number of paired peaks: 621 WARNING @ Sun, 21 Jun 2020 17:39:47: Fewer paired peaks (621) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 621 pairs to build model! INFO @ Sun, 21 Jun 2020 17:39:47: start model_add_line... INFO @ Sun, 21 Jun 2020 17:39:47: start X-correlation... INFO @ Sun, 21 Jun 2020 17:39:47: end of X-cor INFO @ Sun, 21 Jun 2020 17:39:47: #2 finished! INFO @ Sun, 21 Jun 2020 17:39:47: #2 predicted fragment length is 51 bps INFO @ Sun, 21 Jun 2020 17:39:47: #2 alternative fragment length(s) may be 3,51 bps INFO @ Sun, 21 Jun 2020 17:39:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1166568/SRX1166568.05_model.r WARNING @ Sun, 21 Jun 2020 17:39:47: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:39:47: #2 You may need to consider one of the other alternative d(s): 3,51 WARNING @ Sun, 21 Jun 2020 17:39:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 17:39:47: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:39:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:39:49: 11000000 INFO @ Sun, 21 Jun 2020 17:39:52: 7000000 INFO @ Sun, 21 Jun 2020 17:39:56: 12000000 INFO @ Sun, 21 Jun 2020 17:39:59: 8000000 INFO @ Sun, 21 Jun 2020 17:40:03: 13000000 INFO @ Sun, 21 Jun 2020 17:40:06: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:40:10: 14000000 INFO @ Sun, 21 Jun 2020 17:40:13: 10000000 INFO @ Sun, 21 Jun 2020 17:40:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:40:18: 15000000 INFO @ Sun, 21 Jun 2020 17:40:19: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:40:19: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:40:19: #1 total tags in treatment: 15159600 INFO @ Sun, 21 Jun 2020 17:40:19: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:40:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 17:40:20: #1 tags after filtering in treatment: 15159538 INFO @ Sun, 21 Jun 2020 17:40:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:40:20: #1 finished! INFO @ Sun, 21 Jun 2020 17:40:20: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:40:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:40:20: 11000000 INFO @ Sun, 21 Jun 2020 17:40:21: #2 number of paired peaks: 621 WARNING @ Sun, 21 Jun 2020 17:40:21: Fewer paired peaks (621) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 621 pairs to build model! INFO @ Sun, 21 Jun 2020 17:40:21: start model_add_line... INFO @ Sun, 21 Jun 2020 17:40:21: start X-correlation... INFO @ Sun, 21 Jun 2020 17:40:21: end of X-cor INFO @ Sun, 21 Jun 2020 17:40:21: #2 finished! INFO @ Sun, 21 Jun 2020 17:40:21: #2 predicted fragment length is 51 bps INFO @ Sun, 21 Jun 2020 17:40:21: #2 alternative fragment length(s) may be 3,51 bps INFO @ Sun, 21 Jun 2020 17:40:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1166568/SRX1166568.10_model.r WARNING @ Sun, 21 Jun 2020 17:40:21: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:40:21: #2 You may need to consider one of the other alternative d(s): 3,51 WARNING @ Sun, 21 Jun 2020 17:40:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 17:40:21: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:40:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:40:27: 12000000 INFO @ Sun, 21 Jun 2020 17:40:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1166568/SRX1166568.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:40:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1166568/SRX1166568.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:40:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1166568/SRX1166568.05_summits.bed INFO @ Sun, 21 Jun 2020 17:40:31: Done! pass1 - making usageList (583 chroms): 1 millis pass2 - checking and writing primary data (2646 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:40:34: 13000000 INFO @ Sun, 21 Jun 2020 17:40:40: 14000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:40:47: 15000000 INFO @ Sun, 21 Jun 2020 17:40:48: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:40:48: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:40:48: #1 total tags in treatment: 15159600 INFO @ Sun, 21 Jun 2020 17:40:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:40:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 17:40:48: #1 tags after filtering in treatment: 15159538 INFO @ Sun, 21 Jun 2020 17:40:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:40:48: #1 finished! INFO @ Sun, 21 Jun 2020 17:40:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:40:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:40:49: #2 number of paired peaks: 621 WARNING @ Sun, 21 Jun 2020 17:40:49: Fewer paired peaks (621) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 621 pairs to build model! INFO @ Sun, 21 Jun 2020 17:40:49: start model_add_line... INFO @ Sun, 21 Jun 2020 17:40:50: start X-correlation... INFO @ Sun, 21 Jun 2020 17:40:50: end of X-cor INFO @ Sun, 21 Jun 2020 17:40:50: #2 finished! INFO @ Sun, 21 Jun 2020 17:40:50: #2 predicted fragment length is 51 bps INFO @ Sun, 21 Jun 2020 17:40:50: #2 alternative fragment length(s) may be 3,51 bps INFO @ Sun, 21 Jun 2020 17:40:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1166568/SRX1166568.20_model.r WARNING @ Sun, 21 Jun 2020 17:40:50: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:40:50: #2 You may need to consider one of the other alternative d(s): 3,51 WARNING @ Sun, 21 Jun 2020 17:40:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 17:40:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:40:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:40:50: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:41:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1166568/SRX1166568.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:41:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1166568/SRX1166568.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:41:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1166568/SRX1166568.10_summits.bed INFO @ Sun, 21 Jun 2020 17:41:05: Done! pass1 - making usageList (514 chroms): 1 millis pass2 - checking and writing primary data (2015 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:41:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:41:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1166568/SRX1166568.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:41:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1166568/SRX1166568.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:41:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1166568/SRX1166568.20_summits.bed INFO @ Sun, 21 Jun 2020 17:41:34: Done! pass1 - making usageList (351 chroms): 2 millis pass2 - checking and writing primary data (789 records, 4 fields): 10 millis CompletedMACS2peakCalling