Job ID = 6451804 SRX = ERX011420 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T06:52:58 prefetch.2.10.7: 1) Downloading 'ERR031141'... 2020-06-21T06:52:58 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T06:58:24 prefetch.2.10.7: HTTPS download succeed 2020-06-21T06:58:25 prefetch.2.10.7: 'ERR031141' is valid 2020-06-21T06:58:25 prefetch.2.10.7: 1) 'ERR031141' was downloaded successfully 2020-06-21T06:59:17 prefetch.2.10.7: 'ERR031141' has 10 unresolved dependencies 2020-06-21T06:59:17 prefetch.2.10.7: 2) Downloading 'ncbi-acc:AE013599.4?vdb-ctx=refseq'... 2020-06-21T06:59:17 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T06:59:33 prefetch.2.10.7: HTTPS download succeed 2020-06-21T06:59:33 prefetch.2.10.7: 2) 'ncbi-acc:AE013599.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T06:59:33 prefetch.2.10.7: 3) Downloading 'ncbi-acc:AE014134.5?vdb-ctx=refseq'... 2020-06-21T06:59:33 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T06:59:51 prefetch.2.10.7: HTTPS download succeed 2020-06-21T06:59:51 prefetch.2.10.7: 3) 'ncbi-acc:AE014134.5?vdb-ctx=refseq' was downloaded successfully 2020-06-21T06:59:51 prefetch.2.10.7: 4) Downloading 'ncbi-acc:AE014135.3?vdb-ctx=refseq'... 2020-06-21T06:59:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:00:03 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:00:03 prefetch.2.10.7: 4) 'ncbi-acc:AE014135.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T07:00:03 prefetch.2.10.7: 5) Downloading 'ncbi-acc:AE014296.4?vdb-ctx=refseq'... 2020-06-21T07:00:03 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:00:19 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:00:19 prefetch.2.10.7: 5) 'ncbi-acc:AE014296.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T07:00:19 prefetch.2.10.7: 6) Downloading 'ncbi-acc:AE014297.2?vdb-ctx=refseq'... 2020-06-21T07:00:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:00:38 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:00:38 prefetch.2.10.7: 6) 'ncbi-acc:AE014297.2?vdb-ctx=refseq' was downloaded successfully 2020-06-21T07:00:38 prefetch.2.10.7: 7) Downloading 'ncbi-acc:AE014298.4?vdb-ctx=refseq'... 2020-06-21T07:00:38 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:00:55 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:00:55 prefetch.2.10.7: 7) 'ncbi-acc:AE014298.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T07:00:55 prefetch.2.10.7: 8) Downloading 'ncbi-acc:CM000457.1?vdb-ctx=refseq'... 2020-06-21T07:00:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:01:07 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:01:07 prefetch.2.10.7: 8) 'ncbi-acc:CM000457.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T07:01:07 prefetch.2.10.7: 9) Downloading 'ncbi-acc:CM000458.1?vdb-ctx=refseq'... 2020-06-21T07:01:07 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:01:20 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:01:20 prefetch.2.10.7: 9) 'ncbi-acc:CM000458.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T07:01:20 prefetch.2.10.7: 10) Downloading 'ncbi-acc:CM000459.1?vdb-ctx=refseq'... 2020-06-21T07:01:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:01:33 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:01:33 prefetch.2.10.7: 10) 'ncbi-acc:CM000459.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T07:01:33 prefetch.2.10.7: 11) Downloading 'ncbi-acc:FA000001.1?vdb-ctx=refseq'... 2020-06-21T07:01:33 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:01:58 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:01:58 prefetch.2.10.7: 11) 'ncbi-acc:FA000001.1?vdb-ctx=refseq' was downloaded successfully Read 37004836 spots for ERR031141/ERR031141.sra Written 37004836 spots for ERR031141/ERR031141.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: 00:05:00 37004836 reads; of these: 37004836 (100.00%) were unpaired; of these: 6588919 (17.81%) aligned 0 times 24623753 (66.54%) aligned exactly 1 time 5792164 (15.65%) aligned >1 times 82.19% overall alignment rate Time searching: 00:05:00 Overall time: 00:05:00 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] 24264224 / 30415917 = 0.7977 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 16:12:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/ERX011420/ERX011420.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/ERX011420/ERX011420.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/ERX011420/ERX011420.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/ERX011420/ERX011420.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 16:12:30: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:12:30: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:12:35: 1000000 INFO @ Sun, 21 Jun 2020 16:12:40: 2000000 INFO @ Sun, 21 Jun 2020 16:12:45: 3000000 INFO @ Sun, 21 Jun 2020 16:12:50: 4000000 INFO @ Sun, 21 Jun 2020 16:12:55: 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 16:13:00: 6000000 INFO @ Sun, 21 Jun 2020 16:13:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/ERX011420/ERX011420.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/ERX011420/ERX011420.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/ERX011420/ERX011420.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/ERX011420/ERX011420.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 16:13:00: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:13:00: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:13:01: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:13:01: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:13:01: #1 total tags in treatment: 6151693 INFO @ Sun, 21 Jun 2020 16:13:01: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:13:01: #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 16:13:01: #1 tags after filtering in treatment: 6151663 INFO @ Sun, 21 Jun 2020 16:13:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:13:01: #1 finished! INFO @ Sun, 21 Jun 2020 16:13:01: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:13:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:13:02: #2 number of paired peaks: 3066 INFO @ Sun, 21 Jun 2020 16:13:02: start model_add_line... INFO @ Sun, 21 Jun 2020 16:13:02: start X-correlation... INFO @ Sun, 21 Jun 2020 16:13:02: end of X-cor INFO @ Sun, 21 Jun 2020 16:13:02: #2 finished! INFO @ Sun, 21 Jun 2020 16:13:02: #2 predicted fragment length is 64 bps INFO @ Sun, 21 Jun 2020 16:13:02: #2 alternative fragment length(s) may be 4,64,561 bps INFO @ Sun, 21 Jun 2020 16:13:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/ERX011420/ERX011420.05_model.r WARNING @ Sun, 21 Jun 2020 16:13:02: #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 16:13:02: #2 You may need to consider one of the other alternative d(s): 4,64,561 WARNING @ Sun, 21 Jun 2020 16:13:02: #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 16:13:02: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:13:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:13:06: 1000000 INFO @ Sun, 21 Jun 2020 16:13:12: 2000000 INFO @ Sun, 21 Jun 2020 16:13:15: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:13:18: 3000000 INFO @ Sun, 21 Jun 2020 16:13:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/ERX011420/ERX011420.05_peaks.xls INFO @ Sun, 21 Jun 2020 16:13:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/ERX011420/ERX011420.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:13:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/ERX011420/ERX011420.05_summits.bed INFO @ Sun, 21 Jun 2020 16:13:22: Done! pass1 - making usageList (711 chroms): 1 millis pass2 - checking and writing primary data (5260 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:13:24: 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 16:13:30: 5000000 INFO @ Sun, 21 Jun 2020 16:13:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/ERX011420/ERX011420.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/ERX011420/ERX011420.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/ERX011420/ERX011420.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/ERX011420/ERX011420.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 16:13:30: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:13:30: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:13:36: 6000000 INFO @ Sun, 21 Jun 2020 16:13:36: 1000000 INFO @ Sun, 21 Jun 2020 16:13:37: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:13:37: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:13:37: #1 total tags in treatment: 6151693 INFO @ Sun, 21 Jun 2020 16:13:37: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:13:37: #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 16:13:37: #1 tags after filtering in treatment: 6151663 INFO @ Sun, 21 Jun 2020 16:13:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:13:37: #1 finished! INFO @ Sun, 21 Jun 2020 16:13:37: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:13:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:13:38: #2 number of paired peaks: 3066 INFO @ Sun, 21 Jun 2020 16:13:38: start model_add_line... INFO @ Sun, 21 Jun 2020 16:13:38: start X-correlation... INFO @ Sun, 21 Jun 2020 16:13:38: end of X-cor INFO @ Sun, 21 Jun 2020 16:13:38: #2 finished! INFO @ Sun, 21 Jun 2020 16:13:38: #2 predicted fragment length is 64 bps INFO @ Sun, 21 Jun 2020 16:13:38: #2 alternative fragment length(s) may be 4,64,561 bps INFO @ Sun, 21 Jun 2020 16:13:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/ERX011420/ERX011420.10_model.r WARNING @ Sun, 21 Jun 2020 16:13:38: #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 16:13:38: #2 You may need to consider one of the other alternative d(s): 4,64,561 WARNING @ Sun, 21 Jun 2020 16:13:38: #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 16:13:38: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:13:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:13:42: 2000000 INFO @ Sun, 21 Jun 2020 16:13:47: 3000000 INFO @ Sun, 21 Jun 2020 16:13:51: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:13:52: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 16:13:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/ERX011420/ERX011420.10_peaks.xls INFO @ Sun, 21 Jun 2020 16:13:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/ERX011420/ERX011420.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:13:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/ERX011420/ERX011420.10_summits.bed INFO @ Sun, 21 Jun 2020 16:13:57: Done! pass1 - making usageList (452 chroms): 1 millis pass2 - checking and writing primary data (1917 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:13:58: 5000000 INFO @ Sun, 21 Jun 2020 16:14:03: 6000000 INFO @ Sun, 21 Jun 2020 16:14:04: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:14:04: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:14:04: #1 total tags in treatment: 6151693 INFO @ Sun, 21 Jun 2020 16:14:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:14:04: #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 16:14:04: #1 tags after filtering in treatment: 6151663 INFO @ Sun, 21 Jun 2020 16:14:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:14:04: #1 finished! INFO @ Sun, 21 Jun 2020 16:14:04: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:14:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:14:05: #2 number of paired peaks: 3066 INFO @ Sun, 21 Jun 2020 16:14:05: start model_add_line... INFO @ Sun, 21 Jun 2020 16:14:05: start X-correlation... INFO @ Sun, 21 Jun 2020 16:14:05: end of X-cor INFO @ Sun, 21 Jun 2020 16:14:05: #2 finished! INFO @ Sun, 21 Jun 2020 16:14:05: #2 predicted fragment length is 64 bps INFO @ Sun, 21 Jun 2020 16:14:05: #2 alternative fragment length(s) may be 4,64,561 bps INFO @ Sun, 21 Jun 2020 16:14:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/ERX011420/ERX011420.20_model.r WARNING @ Sun, 21 Jun 2020 16:14:05: #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 16:14:05: #2 You may need to consider one of the other alternative d(s): 4,64,561 WARNING @ Sun, 21 Jun 2020 16:14:05: #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 16:14:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:14:05: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 16:14:18: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:14:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/ERX011420/ERX011420.20_peaks.xls INFO @ Sun, 21 Jun 2020 16:14:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/ERX011420/ERX011420.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:14:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/ERX011420/ERX011420.20_summits.bed INFO @ Sun, 21 Jun 2020 16:14:24: Done! pass1 - making usageList (265 chroms): 1 millis pass2 - checking and writing primary data (760 records, 4 fields): 10 millis CompletedMACS2peakCalling