Job ID = 6455825 SRX = SRX3011233 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:18:51 prefetch.2.10.7: 1) Downloading 'SRR5834710'... 2020-06-21T10:18:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:20:18 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:20:19 prefetch.2.10.7: 'SRR5834710' is valid 2020-06-21T10:20:19 prefetch.2.10.7: 1) 'SRR5834710' was downloaded successfully 2020-06-21T10:21:10 prefetch.2.10.7: 'SRR5834710' has 10 unresolved dependencies 2020-06-21T10:21:10 prefetch.2.10.7: 2) Downloading 'ncbi-acc:NC_004353.3?vdb-ctx=refseq'... 2020-06-21T10:21:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:21:23 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:21:23 prefetch.2.10.7: 2) 'ncbi-acc:NC_004353.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:21:23 prefetch.2.10.7: 3) Downloading 'ncbi-acc:NC_004354.3?vdb-ctx=refseq'... 2020-06-21T10:21:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:21:41 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:21:41 prefetch.2.10.7: 3) 'ncbi-acc:NC_004354.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:21:41 prefetch.2.10.7: 4) Downloading 'ncbi-acc:NS_000188.1?vdb-ctx=refseq'... 2020-06-21T10:21:41 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:21:56 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:21:56 prefetch.2.10.7: 4) 'ncbi-acc:NS_000188.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:21:56 prefetch.2.10.7: 5) Downloading 'ncbi-acc:NT_033777.2?vdb-ctx=refseq'... 2020-06-21T10:21:56 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:22:12 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:22:12 prefetch.2.10.7: 5) 'ncbi-acc:NT_033777.2?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:22:12 prefetch.2.10.7: 6) Downloading 'ncbi-acc:NT_033778.3?vdb-ctx=refseq'... 2020-06-21T10:22:12 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:22:29 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:22:29 prefetch.2.10.7: 6) 'ncbi-acc:NT_033778.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:22:29 prefetch.2.10.7: 7) Downloading 'ncbi-acc:NT_033779.4?vdb-ctx=refseq'... 2020-06-21T10:22:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:22:46 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:22:46 prefetch.2.10.7: 7) 'ncbi-acc:NT_033779.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:22:46 prefetch.2.10.7: 8) Downloading 'ncbi-acc:NT_037436.3?vdb-ctx=refseq'... 2020-06-21T10:22:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:23:05 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:23:05 prefetch.2.10.7: 8) 'ncbi-acc:NT_037436.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:23:05 prefetch.2.10.7: 9) Downloading 'ncbi-acc:NW_001848856.1?vdb-ctx=refseq'... 2020-06-21T10:23:05 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:23:18 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:23:18 prefetch.2.10.7: 9) 'ncbi-acc:NW_001848856.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:23:18 prefetch.2.10.7: 10) Downloading 'ncbi-acc:NW_001848857.1?vdb-ctx=refseq'... 2020-06-21T10:23:18 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:23:31 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:23:31 prefetch.2.10.7: 10) 'ncbi-acc:NW_001848857.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:23:31 prefetch.2.10.7: 11) Downloading 'ncbi-acc:NW_001848858.1?vdb-ctx=refseq'... 2020-06-21T10:23:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:23:44 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:23:44 prefetch.2.10.7: 11) 'ncbi-acc:NW_001848858.1?vdb-ctx=refseq' was downloaded successfully Read 24550275 spots for SRR5834710/SRR5834710.sra Written 24550275 spots for SRR5834710/SRR5834710.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: 00:04:42 24550275 reads; of these: 24550275 (100.00%) were unpaired; of these: 7747147 (31.56%) aligned 0 times 11777687 (47.97%) aligned exactly 1 time 5025441 (20.47%) aligned >1 times 68.44% overall alignment rate Time searching: 00:04:42 Overall time: 00:04:42 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 8 files... [bam_rmdupse_core] 7052611 / 16803128 = 0.4197 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 19:32:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3011233/SRX3011233.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3011233/SRX3011233.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3011233/SRX3011233.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3011233/SRX3011233.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 19:32:35: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:32:35: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:32:40: 1000000 INFO @ Sun, 21 Jun 2020 19:32:44: 2000000 INFO @ Sun, 21 Jun 2020 19:32:49: 3000000 INFO @ Sun, 21 Jun 2020 19:32:53: 4000000 INFO @ Sun, 21 Jun 2020 19:32:58: 5000000 INFO @ Sun, 21 Jun 2020 19:33:02: 6000000 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 19:33:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3011233/SRX3011233.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3011233/SRX3011233.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3011233/SRX3011233.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3011233/SRX3011233.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 19:33:05: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:33:05: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:33:07: 7000000 INFO @ Sun, 21 Jun 2020 19:33:10: 1000000 INFO @ Sun, 21 Jun 2020 19:33:11: 8000000 INFO @ Sun, 21 Jun 2020 19:33:14: 2000000 INFO @ Sun, 21 Jun 2020 19:33:16: 9000000 INFO @ Sun, 21 Jun 2020 19:33:19: 3000000 INFO @ Sun, 21 Jun 2020 19:33:20: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:33:20: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:33:20: #1 total tags in treatment: 9750517 INFO @ Sun, 21 Jun 2020 19:33:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:33:20: #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 19:33:20: #1 tags after filtering in treatment: 9750409 INFO @ Sun, 21 Jun 2020 19:33:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:33:20: #1 finished! INFO @ Sun, 21 Jun 2020 19:33:20: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:33:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:33:21: #2 number of paired peaks: 2709 INFO @ Sun, 21 Jun 2020 19:33:21: start model_add_line... INFO @ Sun, 21 Jun 2020 19:33:21: start X-correlation... INFO @ Sun, 21 Jun 2020 19:33:21: end of X-cor INFO @ Sun, 21 Jun 2020 19:33:21: #2 finished! INFO @ Sun, 21 Jun 2020 19:33:21: #2 predicted fragment length is 64 bps INFO @ Sun, 21 Jun 2020 19:33:21: #2 alternative fragment length(s) may be 3,64 bps INFO @ Sun, 21 Jun 2020 19:33:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3011233/SRX3011233.05_model.r WARNING @ Sun, 21 Jun 2020 19:33:21: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:33:21: #2 You may need to consider one of the other alternative d(s): 3,64 WARNING @ Sun, 21 Jun 2020 19:33:21: #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 19:33:21: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:33:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:33:24: 4000000 INFO @ Sun, 21 Jun 2020 19:33:28: 5000000 INFO @ Sun, 21 Jun 2020 19:33:33: 6000000 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 19:33:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3011233/SRX3011233.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3011233/SRX3011233.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3011233/SRX3011233.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3011233/SRX3011233.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 19:33:35: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:33:35: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:33:37: 7000000 INFO @ Sun, 21 Jun 2020 19:33:40: 1000000 INFO @ Sun, 21 Jun 2020 19:33:41: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:33:42: 8000000 INFO @ Sun, 21 Jun 2020 19:33:44: 2000000 INFO @ Sun, 21 Jun 2020 19:33:47: 9000000 INFO @ Sun, 21 Jun 2020 19:33:49: 3000000 INFO @ Sun, 21 Jun 2020 19:33:51: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:33:51: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:33:51: #1 total tags in treatment: 9750517 INFO @ Sun, 21 Jun 2020 19:33:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:33:51: #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 19:33:51: #1 tags after filtering in treatment: 9750409 INFO @ Sun, 21 Jun 2020 19:33:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:33:51: #1 finished! INFO @ Sun, 21 Jun 2020 19:33:51: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:33:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:33:52: #2 number of paired peaks: 2709 INFO @ Sun, 21 Jun 2020 19:33:52: start model_add_line... INFO @ Sun, 21 Jun 2020 19:33:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3011233/SRX3011233.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:33:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3011233/SRX3011233.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:33:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3011233/SRX3011233.05_summits.bed INFO @ Sun, 21 Jun 2020 19:33:52: Done! INFO @ Sun, 21 Jun 2020 19:33:52: start X-correlation... INFO @ Sun, 21 Jun 2020 19:33:52: end of X-cor INFO @ Sun, 21 Jun 2020 19:33:52: #2 finished! INFO @ Sun, 21 Jun 2020 19:33:52: #2 predicted fragment length is 64 bps INFO @ Sun, 21 Jun 2020 19:33:52: #2 alternative fragment length(s) may be 3,64 bps INFO @ Sun, 21 Jun 2020 19:33:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3011233/SRX3011233.10_model.r WARNING @ Sun, 21 Jun 2020 19:33:52: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:33:52: #2 You may need to consider one of the other alternative d(s): 3,64 WARNING @ Sun, 21 Jun 2020 19:33:52: #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 19:33:52: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:33:52: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (604 chroms): 2 millis pass2 - checking and writing primary data (4360 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:33:54: 4000000 INFO @ Sun, 21 Jun 2020 19:33:58: 5000000 INFO @ Sun, 21 Jun 2020 19:34:03: 6000000 INFO @ Sun, 21 Jun 2020 19:34:07: 7000000 INFO @ Sun, 21 Jun 2020 19:34:12: 8000000 INFO @ Sun, 21 Jun 2020 19:34:13: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:34:16: 9000000 INFO @ Sun, 21 Jun 2020 19:34:20: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:34:20: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:34:20: #1 total tags in treatment: 9750517 INFO @ Sun, 21 Jun 2020 19:34:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:34:20: #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 19:34:20: #1 tags after filtering in treatment: 9750409 INFO @ Sun, 21 Jun 2020 19:34:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:34:20: #1 finished! INFO @ Sun, 21 Jun 2020 19:34:20: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:34:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:34:21: #2 number of paired peaks: 2709 INFO @ Sun, 21 Jun 2020 19:34:21: start model_add_line... INFO @ Sun, 21 Jun 2020 19:34:21: start X-correlation... INFO @ Sun, 21 Jun 2020 19:34:21: end of X-cor INFO @ Sun, 21 Jun 2020 19:34:21: #2 finished! INFO @ Sun, 21 Jun 2020 19:34:21: #2 predicted fragment length is 64 bps INFO @ Sun, 21 Jun 2020 19:34:21: #2 alternative fragment length(s) may be 3,64 bps INFO @ Sun, 21 Jun 2020 19:34:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3011233/SRX3011233.20_model.r WARNING @ Sun, 21 Jun 2020 19:34:21: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:34:21: #2 You may need to consider one of the other alternative d(s): 3,64 WARNING @ Sun, 21 Jun 2020 19:34:21: #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 19:34:21: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:34:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:34:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3011233/SRX3011233.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:34:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3011233/SRX3011233.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:34:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3011233/SRX3011233.10_summits.bed INFO @ Sun, 21 Jun 2020 19:34:23: Done! pass1 - making usageList (534 chroms): 1 millis pass2 - checking and writing primary data (2608 records, 4 fields): 17 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:34:41: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:34:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3011233/SRX3011233.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:34:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3011233/SRX3011233.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:34:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3011233/SRX3011233.20_summits.bed INFO @ Sun, 21 Jun 2020 19:34:51: Done! pass1 - making usageList (371 chroms): 1 millis pass2 - checking and writing primary data (926 records, 4 fields): 11 millis CompletedMACS2peakCalling