Job ID = 6453470 SRX = SRX1166569 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:28:26 prefetch.2.10.7: 1) Downloading 'SRR2189037'... 2020-06-21T08:28:26 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:30:11 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:30:12 prefetch.2.10.7: 'SRR2189037' is valid 2020-06-21T08:30:12 prefetch.2.10.7: 1) 'SRR2189037' was downloaded successfully 2020-06-21T08:31:03 prefetch.2.10.7: 'SRR2189037' has 10 unresolved dependencies 2020-06-21T08:31:03 prefetch.2.10.7: 2) Downloading 'ncbi-acc:NC_004353.3?vdb-ctx=refseq'... 2020-06-21T08:31:03 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:31:15 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:31:15 prefetch.2.10.7: 2) 'ncbi-acc:NC_004353.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T08:31:15 prefetch.2.10.7: 3) Downloading 'ncbi-acc:NC_004354.3?vdb-ctx=refseq'... 2020-06-21T08:31:15 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:31:32 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:31:32 prefetch.2.10.7: 3) 'ncbi-acc:NC_004354.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T08:31:32 prefetch.2.10.7: 4) Downloading 'ncbi-acc:NS_000188.1?vdb-ctx=refseq'... 2020-06-21T08:31:32 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:31:49 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:31:49 prefetch.2.10.7: 4) 'ncbi-acc:NS_000188.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T08:31:49 prefetch.2.10.7: 5) Downloading 'ncbi-acc:NT_033777.2?vdb-ctx=refseq'... 2020-06-21T08:31:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:32:06 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:32:06 prefetch.2.10.7: 5) 'ncbi-acc:NT_033777.2?vdb-ctx=refseq' was downloaded successfully 2020-06-21T08:32:06 prefetch.2.10.7: 6) Downloading 'ncbi-acc:NT_033778.3?vdb-ctx=refseq'... 2020-06-21T08:32:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:32:23 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:32:23 prefetch.2.10.7: 6) 'ncbi-acc:NT_033778.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T08:32:23 prefetch.2.10.7: 7) Downloading 'ncbi-acc:NT_033779.4?vdb-ctx=refseq'... 2020-06-21T08:32:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:32:41 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:32:41 prefetch.2.10.7: 7) 'ncbi-acc:NT_033779.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T08:32:41 prefetch.2.10.7: 8) Downloading 'ncbi-acc:NT_037436.3?vdb-ctx=refseq'... 2020-06-21T08:32:41 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:33:00 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:33:00 prefetch.2.10.7: 8) 'ncbi-acc:NT_037436.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T08:33:00 prefetch.2.10.7: 9) Downloading 'ncbi-acc:NW_001848856.1?vdb-ctx=refseq'... 2020-06-21T08:33:00 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:33:14 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:33:14 prefetch.2.10.7: 9) 'ncbi-acc:NW_001848856.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T08:33:14 prefetch.2.10.7: 10) Downloading 'ncbi-acc:NW_001848857.1?vdb-ctx=refseq'... 2020-06-21T08:33:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:33:27 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:33:27 prefetch.2.10.7: 10) 'ncbi-acc:NW_001848857.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T08:33:27 prefetch.2.10.7: 11) Downloading 'ncbi-acc:NW_001848858.1?vdb-ctx=refseq'... 2020-06-21T08:33:27 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:33:41 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:33:41 prefetch.2.10.7: 11) 'ncbi-acc:NW_001848858.1?vdb-ctx=refseq' was downloaded successfully Read 24763427 spots for SRR2189037/SRR2189037.sra Written 24763427 spots for SRR2189037/SRR2189037.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: 00:05:14 24763427 reads; of these: 24763427 (100.00%) were unpaired; of these: 1098722 (4.44%) aligned 0 times 18621353 (75.20%) aligned exactly 1 time 5043352 (20.37%) aligned >1 times 95.56% overall alignment rate Time searching: 00:05:14 Overall time: 00:05:14 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] 14536038 / 23664705 = 0.6142 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 17:43:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1166569/SRX1166569.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1166569/SRX1166569.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1166569/SRX1166569.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1166569/SRX1166569.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 17:43:55: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:43:55: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:44:00: 1000000 INFO @ Sun, 21 Jun 2020 17:44:06: 2000000 INFO @ Sun, 21 Jun 2020 17:44:11: 3000000 INFO @ Sun, 21 Jun 2020 17:44:17: 4000000 INFO @ Sun, 21 Jun 2020 17:44:22: 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 @ Sun, 21 Jun 2020 17:44:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1166569/SRX1166569.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1166569/SRX1166569.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1166569/SRX1166569.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1166569/SRX1166569.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 17:44:24: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:44:24: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:44:28: 6000000 INFO @ Sun, 21 Jun 2020 17:44:31: 1000000 INFO @ Sun, 21 Jun 2020 17:44:35: 7000000 INFO @ Sun, 21 Jun 2020 17:44:37: 2000000 INFO @ Sun, 21 Jun 2020 17:44:41: 8000000 INFO @ Sun, 21 Jun 2020 17:44:43: 3000000 INFO @ Sun, 21 Jun 2020 17:44:48: 9000000 INFO @ Sun, 21 Jun 2020 17:44:49: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:44:49: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:44:49: #1 total tags in treatment: 9128667 INFO @ Sun, 21 Jun 2020 17:44:49: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:44:49: #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 17:44:49: #1 tags after filtering in treatment: 9128578 INFO @ Sun, 21 Jun 2020 17:44:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:44:49: #1 finished! INFO @ Sun, 21 Jun 2020 17:44:49: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:44:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:44:50: 4000000 INFO @ Sun, 21 Jun 2020 17:44:50: #2 number of paired peaks: 996 WARNING @ Sun, 21 Jun 2020 17:44:50: Fewer paired peaks (996) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 996 pairs to build model! INFO @ Sun, 21 Jun 2020 17:44:50: start model_add_line... INFO @ Sun, 21 Jun 2020 17:44:50: start X-correlation... INFO @ Sun, 21 Jun 2020 17:44:50: end of X-cor INFO @ Sun, 21 Jun 2020 17:44:50: #2 finished! INFO @ Sun, 21 Jun 2020 17:44:50: #2 predicted fragment length is 49 bps INFO @ Sun, 21 Jun 2020 17:44:50: #2 alternative fragment length(s) may be 3,49 bps INFO @ Sun, 21 Jun 2020 17:44:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1166569/SRX1166569.05_model.r WARNING @ Sun, 21 Jun 2020 17:44:50: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:44:50: #2 You may need to consider one of the other alternative d(s): 3,49 WARNING @ Sun, 21 Jun 2020 17:44:50: #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 17:44:50: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:44:50: #3 Pre-compute pvalue-qvalue table... 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 17:44:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1166569/SRX1166569.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1166569/SRX1166569.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1166569/SRX1166569.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1166569/SRX1166569.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 17:44:54: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:44:54: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:44:56: 5000000 INFO @ Sun, 21 Jun 2020 17:45:01: 1000000 INFO @ Sun, 21 Jun 2020 17:45:02: 6000000 INFO @ Sun, 21 Jun 2020 17:45:08: 2000000 INFO @ Sun, 21 Jun 2020 17:45:08: 7000000 INFO @ Sun, 21 Jun 2020 17:45:09: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:45:14: 3000000 INFO @ Sun, 21 Jun 2020 17:45:15: 8000000 INFO @ Sun, 21 Jun 2020 17:45:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1166569/SRX1166569.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:45:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1166569/SRX1166569.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:45:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1166569/SRX1166569.05_summits.bed INFO @ Sun, 21 Jun 2020 17:45:19: Done! pass1 - making usageList (589 chroms): 1 millis pass2 - checking and writing primary data (2739 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:45:20: 4000000 INFO @ Sun, 21 Jun 2020 17:45:21: 9000000 INFO @ Sun, 21 Jun 2020 17:45:22: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:45:22: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:45:22: #1 total tags in treatment: 9128667 INFO @ Sun, 21 Jun 2020 17:45:22: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:45:22: #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 17:45:22: #1 tags after filtering in treatment: 9128578 INFO @ Sun, 21 Jun 2020 17:45:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:45:22: #1 finished! INFO @ Sun, 21 Jun 2020 17:45:22: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:45:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:45:23: #2 number of paired peaks: 996 WARNING @ Sun, 21 Jun 2020 17:45:23: Fewer paired peaks (996) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 996 pairs to build model! INFO @ Sun, 21 Jun 2020 17:45:23: start model_add_line... INFO @ Sun, 21 Jun 2020 17:45:23: start X-correlation... INFO @ Sun, 21 Jun 2020 17:45:23: end of X-cor INFO @ Sun, 21 Jun 2020 17:45:23: #2 finished! INFO @ Sun, 21 Jun 2020 17:45:23: #2 predicted fragment length is 49 bps INFO @ Sun, 21 Jun 2020 17:45:23: #2 alternative fragment length(s) may be 3,49 bps INFO @ Sun, 21 Jun 2020 17:45:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1166569/SRX1166569.10_model.r WARNING @ Sun, 21 Jun 2020 17:45:23: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:45:23: #2 You may need to consider one of the other alternative d(s): 3,49 WARNING @ Sun, 21 Jun 2020 17:45:23: #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 17:45:23: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:45:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:45:27: 5000000 INFO @ Sun, 21 Jun 2020 17:45:33: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:45:39: 7000000 INFO @ Sun, 21 Jun 2020 17:45:43: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:45:45: 8000000 INFO @ Sun, 21 Jun 2020 17:45:50: 9000000 INFO @ Sun, 21 Jun 2020 17:45:51: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 17:45:51: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 17:45:51: #1 total tags in treatment: 9128667 INFO @ Sun, 21 Jun 2020 17:45:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:45:51: #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 17:45:51: #1 tags after filtering in treatment: 9128578 INFO @ Sun, 21 Jun 2020 17:45:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:45:51: #1 finished! INFO @ Sun, 21 Jun 2020 17:45:51: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:45:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:45:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1166569/SRX1166569.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:45:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1166569/SRX1166569.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:45:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1166569/SRX1166569.10_summits.bed INFO @ Sun, 21 Jun 2020 17:45:52: Done! INFO @ Sun, 21 Jun 2020 17:45:52: #2 number of paired peaks: 996 WARNING @ Sun, 21 Jun 2020 17:45:52: Fewer paired peaks (996) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 996 pairs to build model! INFO @ Sun, 21 Jun 2020 17:45:52: start model_add_line... INFO @ Sun, 21 Jun 2020 17:45:52: start X-correlation... pass1 - making usageList (521 chroms): 1 millis pass2 - checking and writing primary data (2036 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:45:52: end of X-cor INFO @ Sun, 21 Jun 2020 17:45:52: #2 finished! INFO @ Sun, 21 Jun 2020 17:45:52: #2 predicted fragment length is 49 bps INFO @ Sun, 21 Jun 2020 17:45:52: #2 alternative fragment length(s) may be 3,49 bps INFO @ Sun, 21 Jun 2020 17:45:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1166569/SRX1166569.20_model.r WARNING @ Sun, 21 Jun 2020 17:45:53: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:45:53: #2 You may need to consider one of the other alternative d(s): 3,49 WARNING @ Sun, 21 Jun 2020 17:45:53: #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 17:45:53: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:45:53: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:46:12: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:46:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1166569/SRX1166569.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:46:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1166569/SRX1166569.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:46:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1166569/SRX1166569.20_summits.bed INFO @ Sun, 21 Jun 2020 17:46:21: Done! pass1 - making usageList (347 chroms): 1 millis pass2 - checking and writing primary data (753 records, 4 fields): 12 millis CompletedMACS2peakCalling