Job ID = 6459299 SRX = SRX661500 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:03:46 prefetch.2.10.7: 1) Downloading 'SRR1525220'... 2020-06-21T13:03:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:06:40 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:06:40 prefetch.2.10.7: 1) 'SRR1525220' was downloaded successfully 2020-06-21T13:07:32 prefetch.2.10.7: 'SRR1525220' has 10 unresolved dependencies 2020-06-21T13:07:32 prefetch.2.10.7: 2) Downloading 'ncbi-acc:AE013599.4?vdb-ctx=refseq'... 2020-06-21T13:07:32 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:07:49 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:07:49 prefetch.2.10.7: 2) 'ncbi-acc:AE013599.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T13:07:49 prefetch.2.10.7: 3) Downloading 'ncbi-acc:AE014134.5?vdb-ctx=refseq'... 2020-06-21T13:07:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:08:07 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:08:07 prefetch.2.10.7: 3) 'ncbi-acc:AE014134.5?vdb-ctx=refseq' was downloaded successfully 2020-06-21T13:08:07 prefetch.2.10.7: 4) Downloading 'ncbi-acc:AE014135.3?vdb-ctx=refseq'... 2020-06-21T13:08:07 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:08:19 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:08:19 prefetch.2.10.7: 4) 'ncbi-acc:AE014135.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T13:08:19 prefetch.2.10.7: 5) Downloading 'ncbi-acc:AE014296.4?vdb-ctx=refseq'... 2020-06-21T13:08:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:08:39 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:08:39 prefetch.2.10.7: 5) 'ncbi-acc:AE014296.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T13:08:39 prefetch.2.10.7: 6) Downloading 'ncbi-acc:AE014297.2?vdb-ctx=refseq'... 2020-06-21T13:08:39 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:08:56 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:08:56 prefetch.2.10.7: 6) 'ncbi-acc:AE014297.2?vdb-ctx=refseq' was downloaded successfully 2020-06-21T13:08:56 prefetch.2.10.7: 7) Downloading 'ncbi-acc:AE014298.4?vdb-ctx=refseq'... 2020-06-21T13:08:56 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:09:13 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:09:13 prefetch.2.10.7: 7) 'ncbi-acc:AE014298.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T13:09:13 prefetch.2.10.7: 8) Downloading 'ncbi-acc:CM000457.1?vdb-ctx=refseq'... 2020-06-21T13:09:13 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:09:26 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:09:26 prefetch.2.10.7: 8) 'ncbi-acc:CM000457.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T13:09:26 prefetch.2.10.7: 9) Downloading 'ncbi-acc:CM000458.1?vdb-ctx=refseq'... 2020-06-21T13:09:26 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:09:40 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:09:40 prefetch.2.10.7: 9) 'ncbi-acc:CM000458.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T13:09:40 prefetch.2.10.7: 10) Downloading 'ncbi-acc:CM000459.1?vdb-ctx=refseq'... 2020-06-21T13:09:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:09:54 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:09:54 prefetch.2.10.7: 10) 'ncbi-acc:CM000459.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T13:09:54 prefetch.2.10.7: 11) Downloading 'ncbi-acc:FA000001.1?vdb-ctx=refseq'... 2020-06-21T13:09:54 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:10:10 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:10:10 prefetch.2.10.7: 11) 'ncbi-acc:FA000001.1?vdb-ctx=refseq' was downloaded successfully Read 21722589 spots for SRR1525220/SRR1525220.sra Written 21722589 spots for SRR1525220/SRR1525220.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: 00:03:23 21722589 reads; of these: 21722589 (100.00%) were unpaired; of these: 13500483 (62.15%) aligned 0 times 4445603 (20.47%) aligned exactly 1 time 3776503 (17.39%) aligned >1 times 37.85% overall alignment rate Time searching: 00:03:23 Overall time: 00:03:23 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_rmdupse_core] 2234437 / 8222106 = 0.2718 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 22:16:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX661500/SRX661500.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX661500/SRX661500.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX661500/SRX661500.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX661500/SRX661500.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 22:16:58: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:16:58: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:17:05: 1000000 INFO @ Sun, 21 Jun 2020 22:17:11: 2000000 INFO @ Sun, 21 Jun 2020 22:17:18: 3000000 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 22:17:24: 4000000 INFO @ Sun, 21 Jun 2020 22:17:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX661500/SRX661500.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX661500/SRX661500.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX661500/SRX661500.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX661500/SRX661500.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 22:17:25: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:17:25: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:17:32: 5000000 INFO @ Sun, 21 Jun 2020 22:17:32: 1000000 INFO @ Sun, 21 Jun 2020 22:17:39: #1 tag size is determined as 47 bps INFO @ Sun, 21 Jun 2020 22:17:39: #1 tag size = 47 INFO @ Sun, 21 Jun 2020 22:17:39: #1 total tags in treatment: 5987669 INFO @ Sun, 21 Jun 2020 22:17:39: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:17:39: #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 22:17:39: #1 tags after filtering in treatment: 5987663 INFO @ Sun, 21 Jun 2020 22:17:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:17:39: #1 finished! INFO @ Sun, 21 Jun 2020 22:17:39: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:17:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:17:39: 2000000 INFO @ Sun, 21 Jun 2020 22:17:40: #2 number of paired peaks: 1561 INFO @ Sun, 21 Jun 2020 22:17:40: start model_add_line... INFO @ Sun, 21 Jun 2020 22:17:40: start X-correlation... INFO @ Sun, 21 Jun 2020 22:17:40: end of X-cor INFO @ Sun, 21 Jun 2020 22:17:40: #2 finished! INFO @ Sun, 21 Jun 2020 22:17:40: #2 predicted fragment length is 46 bps INFO @ Sun, 21 Jun 2020 22:17:40: #2 alternative fragment length(s) may be 3,46 bps INFO @ Sun, 21 Jun 2020 22:17:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX661500/SRX661500.05_model.r WARNING @ Sun, 21 Jun 2020 22:17:40: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:17:40: #2 You may need to consider one of the other alternative d(s): 3,46 WARNING @ Sun, 21 Jun 2020 22:17:40: #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 22:17:40: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:17:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:17:46: 3000000 INFO @ Sun, 21 Jun 2020 22:17:52: 4000000 INFO @ Sun, 21 Jun 2020 22:17:53: #3 Call peaks for each chromosome... 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 22:17:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX661500/SRX661500.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX661500/SRX661500.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX661500/SRX661500.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX661500/SRX661500.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 22:17:55: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:17:55: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:17:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX661500/SRX661500.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:17:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX661500/SRX661500.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:17:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX661500/SRX661500.05_summits.bed INFO @ Sun, 21 Jun 2020 22:17:59: Done! pass1 - making usageList (675 chroms): 2 millis INFO @ Sun, 21 Jun 2020 22:17:59: 5000000 pass2 - checking and writing primary data (2844 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:18:02: 1000000 INFO @ Sun, 21 Jun 2020 22:18:06: #1 tag size is determined as 47 bps INFO @ Sun, 21 Jun 2020 22:18:06: #1 tag size = 47 INFO @ Sun, 21 Jun 2020 22:18:06: #1 total tags in treatment: 5987669 INFO @ Sun, 21 Jun 2020 22:18:06: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:18:06: #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 22:18:07: #1 tags after filtering in treatment: 5987663 INFO @ Sun, 21 Jun 2020 22:18:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:18:07: #1 finished! INFO @ Sun, 21 Jun 2020 22:18:07: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:18:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:18:07: #2 number of paired peaks: 1561 INFO @ Sun, 21 Jun 2020 22:18:07: start model_add_line... INFO @ Sun, 21 Jun 2020 22:18:07: start X-correlation... INFO @ Sun, 21 Jun 2020 22:18:07: end of X-cor INFO @ Sun, 21 Jun 2020 22:18:07: #2 finished! INFO @ Sun, 21 Jun 2020 22:18:07: #2 predicted fragment length is 46 bps INFO @ Sun, 21 Jun 2020 22:18:07: #2 alternative fragment length(s) may be 3,46 bps INFO @ Sun, 21 Jun 2020 22:18:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX661500/SRX661500.10_model.r WARNING @ Sun, 21 Jun 2020 22:18:07: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:18:07: #2 You may need to consider one of the other alternative d(s): 3,46 WARNING @ Sun, 21 Jun 2020 22:18:07: #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 22:18:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:18:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:18:09: 2000000 INFO @ Sun, 21 Jun 2020 22:18:15: 3000000 INFO @ Sun, 21 Jun 2020 22:18:21: 4000000 INFO @ Sun, 21 Jun 2020 22:18:21: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:18:27: 5000000 INFO @ Sun, 21 Jun 2020 22:18:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX661500/SRX661500.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:18:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX661500/SRX661500.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:18:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX661500/SRX661500.10_summits.bed INFO @ Sun, 21 Jun 2020 22:18:28: Done! pass1 - making usageList (561 chroms): 1 millis pass2 - checking and writing primary data (2044 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:18:33: #1 tag size is determined as 47 bps INFO @ Sun, 21 Jun 2020 22:18:33: #1 tag size = 47 INFO @ Sun, 21 Jun 2020 22:18:33: #1 total tags in treatment: 5987669 INFO @ Sun, 21 Jun 2020 22:18:33: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:18:33: #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 22:18:34: #1 tags after filtering in treatment: 5987663 INFO @ Sun, 21 Jun 2020 22:18:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:18:34: #1 finished! INFO @ Sun, 21 Jun 2020 22:18:34: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:18:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:18:34: #2 number of paired peaks: 1561 INFO @ Sun, 21 Jun 2020 22:18:34: start model_add_line... INFO @ Sun, 21 Jun 2020 22:18:34: start X-correlation... INFO @ Sun, 21 Jun 2020 22:18:34: end of X-cor INFO @ Sun, 21 Jun 2020 22:18:34: #2 finished! INFO @ Sun, 21 Jun 2020 22:18:34: #2 predicted fragment length is 46 bps INFO @ Sun, 21 Jun 2020 22:18:34: #2 alternative fragment length(s) may be 3,46 bps INFO @ Sun, 21 Jun 2020 22:18:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX661500/SRX661500.20_model.r WARNING @ Sun, 21 Jun 2020 22:18:34: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:18:34: #2 You may need to consider one of the other alternative d(s): 3,46 WARNING @ Sun, 21 Jun 2020 22:18:34: #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 22:18:34: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:18:34: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:18:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:18:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX661500/SRX661500.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:18:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX661500/SRX661500.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:18:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX661500/SRX661500.20_summits.bed INFO @ Sun, 21 Jun 2020 22:18:54: Done! pass1 - making usageList (318 chroms): 1 millis pass2 - checking and writing primary data (662 records, 4 fields): 9 millis CompletedMACS2peakCalling