Job ID = 6455848 SRX = SRX3011252 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 'SRR5834729'... 2020-06-21T10:18:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:20:49 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:20:50 prefetch.2.10.7: 'SRR5834729' is valid 2020-06-21T10:20:50 prefetch.2.10.7: 1) 'SRR5834729' was downloaded successfully 2020-06-21T10:21:42 prefetch.2.10.7: 'SRR5834729' has 10 unresolved dependencies 2020-06-21T10:21:42 prefetch.2.10.7: 2) Downloading 'ncbi-acc:NC_004353.3?vdb-ctx=refseq'... 2020-06-21T10:21:42 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:21:53 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:21:53 prefetch.2.10.7: 2) 'ncbi-acc:NC_004353.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:21:53 prefetch.2.10.7: 3) Downloading 'ncbi-acc:NC_004354.3?vdb-ctx=refseq'... 2020-06-21T10:21:53 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:22:10 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:22:10 prefetch.2.10.7: 3) 'ncbi-acc:NC_004354.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:22:10 prefetch.2.10.7: 4) Downloading 'ncbi-acc:NS_000188.1?vdb-ctx=refseq'... 2020-06-21T10:22:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:22:25 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:22:25 prefetch.2.10.7: 4) 'ncbi-acc:NS_000188.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:22:25 prefetch.2.10.7: 5) Downloading 'ncbi-acc:NT_033777.2?vdb-ctx=refseq'... 2020-06-21T10:22:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:22:41 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:22:41 prefetch.2.10.7: 5) 'ncbi-acc:NT_033777.2?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:22:41 prefetch.2.10.7: 6) Downloading 'ncbi-acc:NT_033778.3?vdb-ctx=refseq'... 2020-06-21T10:22:41 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:22:58 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:22:58 prefetch.2.10.7: 6) 'ncbi-acc:NT_033778.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:22:58 prefetch.2.10.7: 7) Downloading 'ncbi-acc:NT_033779.4?vdb-ctx=refseq'... 2020-06-21T10:22:58 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:23:14 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:23:14 prefetch.2.10.7: 7) 'ncbi-acc:NT_033779.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:23:14 prefetch.2.10.7: 8) Downloading 'ncbi-acc:NT_037436.3?vdb-ctx=refseq'... 2020-06-21T10:23:14 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: 8) 'ncbi-acc:NT_037436.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:23:31 prefetch.2.10.7: 9) Downloading 'ncbi-acc:NW_001848856.1?vdb-ctx=refseq'... 2020-06-21T10:23:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:23:45 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:23:45 prefetch.2.10.7: 9) 'ncbi-acc:NW_001848856.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:23:45 prefetch.2.10.7: 10) Downloading 'ncbi-acc:NW_001848857.1?vdb-ctx=refseq'... 2020-06-21T10:23:45 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:23:58 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:23:58 prefetch.2.10.7: 10) 'ncbi-acc:NW_001848857.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:23:58 prefetch.2.10.7: 11) Downloading 'ncbi-acc:NW_001848858.1?vdb-ctx=refseq'... 2020-06-21T10:23:58 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:24:11 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:24:11 prefetch.2.10.7: 11) 'ncbi-acc:NW_001848858.1?vdb-ctx=refseq' was downloaded successfully Read 18026227 spots for SRR5834729/SRR5834729.sra Written 18026227 spots for SRR5834729/SRR5834729.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: 00:05:29 18026227 reads; of these: 18026227 (100.00%) were unpaired; of these: 318817 (1.77%) aligned 0 times 13443230 (74.58%) aligned exactly 1 time 4264180 (23.66%) aligned >1 times 98.23% overall alignment rate Time searching: 00:05:29 Overall time: 00:05:29 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] 6083765 / 17707410 = 0.3436 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 19:36:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3011252/SRX3011252.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3011252/SRX3011252.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3011252/SRX3011252.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3011252/SRX3011252.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 19:36:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:36:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:36:16: 1000000 INFO @ Sun, 21 Jun 2020 19:36:23: 2000000 INFO @ Sun, 21 Jun 2020 19:36:29: 3000000 INFO @ Sun, 21 Jun 2020 19:36:36: 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 19:36:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3011252/SRX3011252.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3011252/SRX3011252.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3011252/SRX3011252.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3011252/SRX3011252.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 19:36:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:36:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:36:43: 5000000 INFO @ Sun, 21 Jun 2020 19:36:47: 1000000 INFO @ Sun, 21 Jun 2020 19:36:49: 6000000 INFO @ Sun, 21 Jun 2020 19:36:54: 2000000 INFO @ Sun, 21 Jun 2020 19:36:56: 7000000 INFO @ Sun, 21 Jun 2020 19:37:00: 3000000 INFO @ Sun, 21 Jun 2020 19:37:03: 8000000 INFO @ Sun, 21 Jun 2020 19:37:07: 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 19:37:09: 9000000 INFO @ Sun, 21 Jun 2020 19:37:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3011252/SRX3011252.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3011252/SRX3011252.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3011252/SRX3011252.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3011252/SRX3011252.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 19:37:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:37:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:37:14: 5000000 INFO @ Sun, 21 Jun 2020 19:37:17: 10000000 INFO @ Sun, 21 Jun 2020 19:37:17: 1000000 INFO @ Sun, 21 Jun 2020 19:37:21: 6000000 INFO @ Sun, 21 Jun 2020 19:37:24: 11000000 INFO @ Sun, 21 Jun 2020 19:37:24: 2000000 INFO @ Sun, 21 Jun 2020 19:37:28: 7000000 INFO @ Sun, 21 Jun 2020 19:37:28: #1 tag size is determined as 80 bps INFO @ Sun, 21 Jun 2020 19:37:28: #1 tag size = 80 INFO @ Sun, 21 Jun 2020 19:37:28: #1 total tags in treatment: 11623645 INFO @ Sun, 21 Jun 2020 19:37:28: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:37:28: #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 19:37:29: #1 tags after filtering in treatment: 11623496 INFO @ Sun, 21 Jun 2020 19:37:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:37:29: #1 finished! INFO @ Sun, 21 Jun 2020 19:37:29: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:37:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:37:30: #2 number of paired peaks: 1826 INFO @ Sun, 21 Jun 2020 19:37:30: start model_add_line... INFO @ Sun, 21 Jun 2020 19:37:30: start X-correlation... INFO @ Sun, 21 Jun 2020 19:37:30: end of X-cor INFO @ Sun, 21 Jun 2020 19:37:30: #2 finished! INFO @ Sun, 21 Jun 2020 19:37:30: #2 predicted fragment length is 150 bps INFO @ Sun, 21 Jun 2020 19:37:30: #2 alternative fragment length(s) may be 150 bps INFO @ Sun, 21 Jun 2020 19:37:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3011252/SRX3011252.05_model.r WARNING @ Sun, 21 Jun 2020 19:37:30: #2 Since the d (150) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:37:30: #2 You may need to consider one of the other alternative d(s): 150 WARNING @ Sun, 21 Jun 2020 19:37:30: #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 19:37:30: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:37:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:37:31: 3000000 INFO @ Sun, 21 Jun 2020 19:37:35: 8000000 INFO @ Sun, 21 Jun 2020 19:37:38: 4000000 INFO @ Sun, 21 Jun 2020 19:37:42: 9000000 INFO @ Sun, 21 Jun 2020 19:37:45: 5000000 INFO @ Sun, 21 Jun 2020 19:37:49: 10000000 INFO @ Sun, 21 Jun 2020 19:37:52: 6000000 INFO @ Sun, 21 Jun 2020 19:37:56: 11000000 INFO @ Sun, 21 Jun 2020 19:37:59: 7000000 INFO @ Sun, 21 Jun 2020 19:38:00: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:38:00: #1 tag size is determined as 80 bps INFO @ Sun, 21 Jun 2020 19:38:00: #1 tag size = 80 INFO @ Sun, 21 Jun 2020 19:38:00: #1 total tags in treatment: 11623645 INFO @ Sun, 21 Jun 2020 19:38:00: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:38:00: #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 19:38:01: #1 tags after filtering in treatment: 11623496 INFO @ Sun, 21 Jun 2020 19:38:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:38:01: #1 finished! INFO @ Sun, 21 Jun 2020 19:38:01: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:38:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:38:02: #2 number of paired peaks: 1826 INFO @ Sun, 21 Jun 2020 19:38:02: start model_add_line... INFO @ Sun, 21 Jun 2020 19:38:02: start X-correlation... INFO @ Sun, 21 Jun 2020 19:38:02: end of X-cor INFO @ Sun, 21 Jun 2020 19:38:02: #2 finished! INFO @ Sun, 21 Jun 2020 19:38:02: #2 predicted fragment length is 150 bps INFO @ Sun, 21 Jun 2020 19:38:02: #2 alternative fragment length(s) may be 150 bps INFO @ Sun, 21 Jun 2020 19:38:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3011252/SRX3011252.10_model.r WARNING @ Sun, 21 Jun 2020 19:38:02: #2 Since the d (150) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:38:02: #2 You may need to consider one of the other alternative d(s): 150 WARNING @ Sun, 21 Jun 2020 19:38:02: #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 19:38:02: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:38:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:38:06: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:38:13: 9000000 INFO @ Sun, 21 Jun 2020 19:38:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3011252/SRX3011252.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:38:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3011252/SRX3011252.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:38:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3011252/SRX3011252.05_summits.bed INFO @ Sun, 21 Jun 2020 19:38:14: Done! pass1 - making usageList (482 chroms): 2 millis pass2 - checking and writing primary data (8052 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:38:20: 10000000 INFO @ Sun, 21 Jun 2020 19:38:27: 11000000 INFO @ Sun, 21 Jun 2020 19:38:31: #1 tag size is determined as 80 bps INFO @ Sun, 21 Jun 2020 19:38:31: #1 tag size = 80 INFO @ Sun, 21 Jun 2020 19:38:31: #1 total tags in treatment: 11623645 INFO @ Sun, 21 Jun 2020 19:38:31: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:38:31: #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 19:38:31: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:38:31: #1 tags after filtering in treatment: 11623496 INFO @ Sun, 21 Jun 2020 19:38:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:38:31: #1 finished! INFO @ Sun, 21 Jun 2020 19:38:31: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:38:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:38:32: #2 number of paired peaks: 1826 INFO @ Sun, 21 Jun 2020 19:38:32: start model_add_line... INFO @ Sun, 21 Jun 2020 19:38:33: start X-correlation... INFO @ Sun, 21 Jun 2020 19:38:33: end of X-cor INFO @ Sun, 21 Jun 2020 19:38:33: #2 finished! INFO @ Sun, 21 Jun 2020 19:38:33: #2 predicted fragment length is 150 bps INFO @ Sun, 21 Jun 2020 19:38:33: #2 alternative fragment length(s) may be 150 bps INFO @ Sun, 21 Jun 2020 19:38:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3011252/SRX3011252.20_model.r WARNING @ Sun, 21 Jun 2020 19:38:33: #2 Since the d (150) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:38:33: #2 You may need to consider one of the other alternative d(s): 150 WARNING @ Sun, 21 Jun 2020 19:38:33: #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 19:38:33: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:38:33: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:38:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3011252/SRX3011252.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:38:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3011252/SRX3011252.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:38:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3011252/SRX3011252.10_summits.bed INFO @ Sun, 21 Jun 2020 19:38:45: Done! pass1 - making usageList (377 chroms): 1 millis pass2 - checking and writing primary data (4641 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:39:02: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:39:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3011252/SRX3011252.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:39:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3011252/SRX3011252.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:39:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3011252/SRX3011252.20_summits.bed INFO @ Sun, 21 Jun 2020 19:39:16: Done! pass1 - making usageList (219 chroms): 1 millis pass2 - checking and writing primary data (1838 records, 4 fields): 9 millis CompletedMACS2peakCalling