Job ID = 6455841 SRX = SRX3011248 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:23:36 prefetch.2.10.7: 1) Downloading 'SRR5834725'... 2020-06-21T10:23:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:26:30 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:26:30 prefetch.2.10.7: 1) 'SRR5834725' was downloaded successfully 2020-06-21T10:27:22 prefetch.2.10.7: 'SRR5834725' has 10 unresolved dependencies 2020-06-21T10:27:22 prefetch.2.10.7: 2) Downloading 'ncbi-acc:NC_004353.3?vdb-ctx=refseq'... 2020-06-21T10:27:22 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:27:34 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:27:34 prefetch.2.10.7: 2) 'ncbi-acc:NC_004353.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:27:34 prefetch.2.10.7: 3) Downloading 'ncbi-acc:NC_004354.3?vdb-ctx=refseq'... 2020-06-21T10:27:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:27:52 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:27:52 prefetch.2.10.7: 3) 'ncbi-acc:NC_004354.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:27:52 prefetch.2.10.7: 4) Downloading 'ncbi-acc:NS_000188.1?vdb-ctx=refseq'... 2020-06-21T10:27:52 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:28:09 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:28:09 prefetch.2.10.7: 4) 'ncbi-acc:NS_000188.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:28:09 prefetch.2.10.7: 5) Downloading 'ncbi-acc:NT_033777.2?vdb-ctx=refseq'... 2020-06-21T10:28:09 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:28:25 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:28:25 prefetch.2.10.7: 5) 'ncbi-acc:NT_033777.2?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:28:25 prefetch.2.10.7: 6) Downloading 'ncbi-acc:NT_033778.3?vdb-ctx=refseq'... 2020-06-21T10:28:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:28:44 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:28:44 prefetch.2.10.7: 6) 'ncbi-acc:NT_033778.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:28:44 prefetch.2.10.7: 7) Downloading 'ncbi-acc:NT_033779.4?vdb-ctx=refseq'... 2020-06-21T10:28:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:29:00 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:29:00 prefetch.2.10.7: 7) 'ncbi-acc:NT_033779.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:29:00 prefetch.2.10.7: 8) Downloading 'ncbi-acc:NT_037436.3?vdb-ctx=refseq'... 2020-06-21T10:29:00 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:29:16 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:29:16 prefetch.2.10.7: 8) 'ncbi-acc:NT_037436.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:29:16 prefetch.2.10.7: 9) Downloading 'ncbi-acc:NW_001848856.1?vdb-ctx=refseq'... 2020-06-21T10:29:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:29:30 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:29:30 prefetch.2.10.7: 9) 'ncbi-acc:NW_001848856.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:29:30 prefetch.2.10.7: 10) Downloading 'ncbi-acc:NW_001848857.1?vdb-ctx=refseq'... 2020-06-21T10:29:30 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:29:43 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:29:43 prefetch.2.10.7: 10) 'ncbi-acc:NW_001848857.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:29:43 prefetch.2.10.7: 11) Downloading 'ncbi-acc:NW_001848858.1?vdb-ctx=refseq'... 2020-06-21T10:29:43 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:29:57 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:29:57 prefetch.2.10.7: 11) 'ncbi-acc:NW_001848858.1?vdb-ctx=refseq' was downloaded successfully Read 18360537 spots for SRR5834725/SRR5834725.sra Written 18360537 spots for SRR5834725/SRR5834725.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: 00:05:18 18360537 reads; of these: 18360537 (100.00%) were unpaired; of these: 1043311 (5.68%) aligned 0 times 13639026 (74.28%) aligned exactly 1 time 3678200 (20.03%) aligned >1 times 94.32% overall alignment rate Time searching: 00:05:18 Overall time: 00:05:18 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] 5587235 / 17317226 = 0.3226 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 19:41:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3011248/SRX3011248.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3011248/SRX3011248.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3011248/SRX3011248.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3011248/SRX3011248.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 19:41:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:41:22: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:41:29: 1000000 INFO @ Sun, 21 Jun 2020 19:41:35: 2000000 INFO @ Sun, 21 Jun 2020 19:41:41: 3000000 INFO @ Sun, 21 Jun 2020 19:41:48: 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 19:41:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3011248/SRX3011248.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3011248/SRX3011248.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3011248/SRX3011248.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3011248/SRX3011248.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 19:41:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:41:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:41:54: 5000000 INFO @ Sun, 21 Jun 2020 19:42:00: 1000000 INFO @ Sun, 21 Jun 2020 19:42:01: 6000000 INFO @ Sun, 21 Jun 2020 19:42:08: 2000000 INFO @ Sun, 21 Jun 2020 19:42:09: 7000000 INFO @ Sun, 21 Jun 2020 19:42:15: 3000000 INFO @ Sun, 21 Jun 2020 19:42:16: 8000000 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 19:42:22: 4000000 INFO @ Sun, 21 Jun 2020 19:42:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3011248/SRX3011248.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3011248/SRX3011248.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3011248/SRX3011248.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3011248/SRX3011248.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 19:42:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:42:22: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:42:23: 9000000 INFO @ Sun, 21 Jun 2020 19:42:29: 5000000 INFO @ Sun, 21 Jun 2020 19:42:30: 1000000 INFO @ Sun, 21 Jun 2020 19:42:31: 10000000 INFO @ Sun, 21 Jun 2020 19:42:37: 6000000 INFO @ Sun, 21 Jun 2020 19:42:37: 2000000 INFO @ Sun, 21 Jun 2020 19:42:38: 11000000 INFO @ Sun, 21 Jun 2020 19:42:44: #1 tag size is determined as 80 bps INFO @ Sun, 21 Jun 2020 19:42:44: #1 tag size = 80 INFO @ Sun, 21 Jun 2020 19:42:44: #1 total tags in treatment: 11729991 INFO @ Sun, 21 Jun 2020 19:42:44: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:42:44: #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 19:42:44: 7000000 INFO @ Sun, 21 Jun 2020 19:42:44: #1 tags after filtering in treatment: 11729846 INFO @ Sun, 21 Jun 2020 19:42:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:42:44: #1 finished! INFO @ Sun, 21 Jun 2020 19:42:44: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:42:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:42:44: 3000000 INFO @ Sun, 21 Jun 2020 19:42:45: #2 number of paired peaks: 1395 INFO @ Sun, 21 Jun 2020 19:42:45: start model_add_line... INFO @ Sun, 21 Jun 2020 19:42:45: start X-correlation... INFO @ Sun, 21 Jun 2020 19:42:45: end of X-cor INFO @ Sun, 21 Jun 2020 19:42:45: #2 finished! INFO @ Sun, 21 Jun 2020 19:42:45: #2 predicted fragment length is 160 bps INFO @ Sun, 21 Jun 2020 19:42:45: #2 alternative fragment length(s) may be 160 bps INFO @ Sun, 21 Jun 2020 19:42:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3011248/SRX3011248.05_model.r WARNING @ Sun, 21 Jun 2020 19:42:45: #2 Since the d (160) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:42:45: #2 You may need to consider one of the other alternative d(s): 160 WARNING @ Sun, 21 Jun 2020 19:42:45: #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 19:42:45: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:42:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:42:51: 8000000 INFO @ Sun, 21 Jun 2020 19:42:51: 4000000 INFO @ Sun, 21 Jun 2020 19:42:58: 9000000 INFO @ Sun, 21 Jun 2020 19:42:58: 5000000 INFO @ Sun, 21 Jun 2020 19:43:06: 6000000 INFO @ Sun, 21 Jun 2020 19:43:06: 10000000 INFO @ Sun, 21 Jun 2020 19:43:12: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:43:13: 7000000 INFO @ Sun, 21 Jun 2020 19:43:13: 11000000 INFO @ Sun, 21 Jun 2020 19:43:19: #1 tag size is determined as 80 bps INFO @ Sun, 21 Jun 2020 19:43:19: #1 tag size = 80 INFO @ Sun, 21 Jun 2020 19:43:19: #1 total tags in treatment: 11729991 INFO @ Sun, 21 Jun 2020 19:43:19: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:43:19: #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 19:43:19: #1 tags after filtering in treatment: 11729846 INFO @ Sun, 21 Jun 2020 19:43:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:43:19: #1 finished! INFO @ Sun, 21 Jun 2020 19:43:19: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:43:19: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:43:20: 8000000 INFO @ Sun, 21 Jun 2020 19:43:20: #2 number of paired peaks: 1395 INFO @ Sun, 21 Jun 2020 19:43:20: start model_add_line... INFO @ Sun, 21 Jun 2020 19:43:20: start X-correlation... INFO @ Sun, 21 Jun 2020 19:43:20: end of X-cor INFO @ Sun, 21 Jun 2020 19:43:20: #2 finished! INFO @ Sun, 21 Jun 2020 19:43:20: #2 predicted fragment length is 160 bps INFO @ Sun, 21 Jun 2020 19:43:20: #2 alternative fragment length(s) may be 160 bps INFO @ Sun, 21 Jun 2020 19:43:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3011248/SRX3011248.10_model.r WARNING @ Sun, 21 Jun 2020 19:43:20: #2 Since the d (160) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:43:20: #2 You may need to consider one of the other alternative d(s): 160 WARNING @ Sun, 21 Jun 2020 19:43:20: #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 19:43:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:43:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:43:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3011248/SRX3011248.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:43:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3011248/SRX3011248.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:43:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3011248/SRX3011248.05_summits.bed INFO @ Sun, 21 Jun 2020 19:43:26: Done! pass1 - making usageList (532 chroms): 2 millis pass2 - checking and writing primary data (8171 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:43:27: 9000000 INFO @ Sun, 21 Jun 2020 19:43:34: 10000000 INFO @ Sun, 21 Jun 2020 19:43:41: 11000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:43:46: #1 tag size is determined as 80 bps INFO @ Sun, 21 Jun 2020 19:43:46: #1 tag size = 80 INFO @ Sun, 21 Jun 2020 19:43:46: #1 total tags in treatment: 11729991 INFO @ Sun, 21 Jun 2020 19:43:46: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:43:46: #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 19:43:47: #1 tags after filtering in treatment: 11729846 INFO @ Sun, 21 Jun 2020 19:43:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:43:47: #1 finished! INFO @ Sun, 21 Jun 2020 19:43:47: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:43:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:43:48: #2 number of paired peaks: 1395 INFO @ Sun, 21 Jun 2020 19:43:48: start model_add_line... INFO @ Sun, 21 Jun 2020 19:43:48: start X-correlation... INFO @ Sun, 21 Jun 2020 19:43:48: end of X-cor INFO @ Sun, 21 Jun 2020 19:43:48: #2 finished! INFO @ Sun, 21 Jun 2020 19:43:48: #2 predicted fragment length is 160 bps INFO @ Sun, 21 Jun 2020 19:43:48: #2 alternative fragment length(s) may be 160 bps INFO @ Sun, 21 Jun 2020 19:43:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3011248/SRX3011248.20_model.r WARNING @ Sun, 21 Jun 2020 19:43:48: #2 Since the d (160) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:43:48: #2 You may need to consider one of the other alternative d(s): 160 WARNING @ Sun, 21 Jun 2020 19:43:48: #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 19:43:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:43:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:43:49: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:44:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3011248/SRX3011248.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:44:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3011248/SRX3011248.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:44:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3011248/SRX3011248.10_summits.bed INFO @ Sun, 21 Jun 2020 19:44:03: Done! pass1 - making usageList (361 chroms): 2 millis pass2 - checking and writing primary data (4239 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:44:18: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:44:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3011248/SRX3011248.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:44:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3011248/SRX3011248.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:44:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3011248/SRX3011248.20_summits.bed INFO @ Sun, 21 Jun 2020 19:44:33: Done! pass1 - making usageList (186 chroms): 1 millis pass2 - checking and writing primary data (1916 records, 4 fields): 8 millis CompletedMACS2peakCalling