Job ID = 6455840 SRX = SRX3011247 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:16:06 prefetch.2.10.7: 1) Downloading 'SRR5834724'... 2020-06-21T10:16:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:18:47 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:18:48 prefetch.2.10.7: 'SRR5834724' is valid 2020-06-21T10:18:48 prefetch.2.10.7: 1) 'SRR5834724' was downloaded successfully 2020-06-21T10:19:40 prefetch.2.10.7: 'SRR5834724' has 10 unresolved dependencies 2020-06-21T10:19:40 prefetch.2.10.7: 2) Downloading 'ncbi-acc:NC_004353.3?vdb-ctx=refseq'... 2020-06-21T10:19:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:19:52 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:19:52 prefetch.2.10.7: 2) 'ncbi-acc:NC_004353.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:19:52 prefetch.2.10.7: 3) Downloading 'ncbi-acc:NC_004354.3?vdb-ctx=refseq'... 2020-06-21T10:19:52 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:20:09 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:20:09 prefetch.2.10.7: 3) 'ncbi-acc:NC_004354.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:20:09 prefetch.2.10.7: 4) Downloading 'ncbi-acc:NS_000188.1?vdb-ctx=refseq'... 2020-06-21T10:20:09 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:20:24 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:20:24 prefetch.2.10.7: 4) 'ncbi-acc:NS_000188.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:20:24 prefetch.2.10.7: 5) Downloading 'ncbi-acc:NT_033777.2?vdb-ctx=refseq'... 2020-06-21T10:20:24 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:21:41 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:21:41 prefetch.2.10.7: 5) 'ncbi-acc:NT_033777.2?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:21:41 prefetch.2.10.7: 6) Downloading 'ncbi-acc:NT_033778.3?vdb-ctx=refseq'... 2020-06-21T10:21:41 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:21:58 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:21:58 prefetch.2.10.7: 6) 'ncbi-acc:NT_033778.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:21:58 prefetch.2.10.7: 7) Downloading 'ncbi-acc:NT_033779.4?vdb-ctx=refseq'... 2020-06-21T10:21:58 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:22:18 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:22:18 prefetch.2.10.7: 7) 'ncbi-acc:NT_033779.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:22:18 prefetch.2.10.7: 8) Downloading 'ncbi-acc:NT_037436.3?vdb-ctx=refseq'... 2020-06-21T10:22:18 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:22:38 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:22:38 prefetch.2.10.7: 8) 'ncbi-acc:NT_037436.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:22:38 prefetch.2.10.7: 9) Downloading 'ncbi-acc:NW_001848856.1?vdb-ctx=refseq'... 2020-06-21T10:22:38 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:22:51 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:22:51 prefetch.2.10.7: 9) 'ncbi-acc:NW_001848856.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:22:51 prefetch.2.10.7: 10) Downloading 'ncbi-acc:NW_001848857.1?vdb-ctx=refseq'... 2020-06-21T10:22:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:23:03 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:23:03 prefetch.2.10.7: 10) 'ncbi-acc:NW_001848857.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:23:03 prefetch.2.10.7: 11) Downloading 'ncbi-acc:NW_001848858.1?vdb-ctx=refseq'... 2020-06-21T10:23:03 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:23:17 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:23:17 prefetch.2.10.7: 11) 'ncbi-acc:NW_001848858.1?vdb-ctx=refseq' was downloaded successfully Read 15792541 spots for SRR5834724/SRR5834724.sra Written 15792541 spots for SRR5834724/SRR5834724.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: 00:05:03 15792541 reads; of these: 15792541 (100.00%) were unpaired; of these: 901362 (5.71%) aligned 0 times 11685223 (73.99%) aligned exactly 1 time 3205956 (20.30%) aligned >1 times 94.29% overall alignment rate Time searching: 00:05:03 Overall time: 00:05:03 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] 3542757 / 14891179 = 0.2379 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 19:34:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3011247/SRX3011247.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3011247/SRX3011247.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3011247/SRX3011247.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3011247/SRX3011247.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 19:34:15: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:34:15: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:34:21: 1000000 INFO @ Sun, 21 Jun 2020 19:34:27: 2000000 INFO @ Sun, 21 Jun 2020 19:34:33: 3000000 INFO @ Sun, 21 Jun 2020 19:34:39: 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 19:34:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3011247/SRX3011247.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3011247/SRX3011247.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3011247/SRX3011247.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3011247/SRX3011247.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 19:34:45: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:34:45: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:34:45: 5000000 INFO @ Sun, 21 Jun 2020 19:34:51: 6000000 INFO @ Sun, 21 Jun 2020 19:34:52: 1000000 INFO @ Sun, 21 Jun 2020 19:34:58: 7000000 INFO @ Sun, 21 Jun 2020 19:34:59: 2000000 INFO @ Sun, 21 Jun 2020 19:35:04: 8000000 INFO @ Sun, 21 Jun 2020 19:35:06: 3000000 INFO @ Sun, 21 Jun 2020 19:35:10: 9000000 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 19:35:14: 4000000 INFO @ Sun, 21 Jun 2020 19:35:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3011247/SRX3011247.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3011247/SRX3011247.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3011247/SRX3011247.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3011247/SRX3011247.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 19:35:15: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:35:15: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:35:17: 10000000 INFO @ Sun, 21 Jun 2020 19:35:21: 5000000 INFO @ Sun, 21 Jun 2020 19:35:22: 1000000 INFO @ Sun, 21 Jun 2020 19:35:23: 11000000 INFO @ Sun, 21 Jun 2020 19:35:25: #1 tag size is determined as 80 bps INFO @ Sun, 21 Jun 2020 19:35:25: #1 tag size = 80 INFO @ Sun, 21 Jun 2020 19:35:25: #1 total tags in treatment: 11348422 INFO @ Sun, 21 Jun 2020 19:35:25: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:35:25: #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 19:35:26: #1 tags after filtering in treatment: 11348233 INFO @ Sun, 21 Jun 2020 19:35:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:35:26: #1 finished! INFO @ Sun, 21 Jun 2020 19:35:26: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:35:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:35:27: #2 number of paired peaks: 1276 INFO @ Sun, 21 Jun 2020 19:35:27: start model_add_line... INFO @ Sun, 21 Jun 2020 19:35:27: start X-correlation... INFO @ Sun, 21 Jun 2020 19:35:27: end of X-cor INFO @ Sun, 21 Jun 2020 19:35:27: #2 finished! INFO @ Sun, 21 Jun 2020 19:35:27: #2 predicted fragment length is 157 bps INFO @ Sun, 21 Jun 2020 19:35:27: #2 alternative fragment length(s) may be 157 bps INFO @ Sun, 21 Jun 2020 19:35:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3011247/SRX3011247.05_model.r WARNING @ Sun, 21 Jun 2020 19:35:27: #2 Since the d (157) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:35:27: #2 You may need to consider one of the other alternative d(s): 157 WARNING @ Sun, 21 Jun 2020 19:35:27: #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 19:35:27: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:35:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:35:29: 6000000 INFO @ Sun, 21 Jun 2020 19:35:29: 2000000 INFO @ Sun, 21 Jun 2020 19:35:37: 7000000 INFO @ Sun, 21 Jun 2020 19:35:37: 3000000 INFO @ Sun, 21 Jun 2020 19:35:44: 8000000 INFO @ Sun, 21 Jun 2020 19:35:44: 4000000 INFO @ Sun, 21 Jun 2020 19:35:51: 9000000 INFO @ Sun, 21 Jun 2020 19:35:52: 5000000 INFO @ Sun, 21 Jun 2020 19:35:55: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:35:59: 10000000 INFO @ Sun, 21 Jun 2020 19:35:59: 6000000 INFO @ Sun, 21 Jun 2020 19:36:06: 11000000 INFO @ Sun, 21 Jun 2020 19:36:07: 7000000 INFO @ Sun, 21 Jun 2020 19:36:09: #1 tag size is determined as 80 bps INFO @ Sun, 21 Jun 2020 19:36:09: #1 tag size = 80 INFO @ Sun, 21 Jun 2020 19:36:09: #1 total tags in treatment: 11348422 INFO @ Sun, 21 Jun 2020 19:36:09: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:36:09: #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 19:36:10: #1 tags after filtering in treatment: 11348233 INFO @ Sun, 21 Jun 2020 19:36:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:36:10: #1 finished! INFO @ Sun, 21 Jun 2020 19:36:10: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:36:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:36:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3011247/SRX3011247.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:36:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3011247/SRX3011247.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:36:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3011247/SRX3011247.05_summits.bed INFO @ Sun, 21 Jun 2020 19:36:10: Done! INFO @ Sun, 21 Jun 2020 19:36:11: #2 number of paired peaks: 1276 INFO @ Sun, 21 Jun 2020 19:36:11: start model_add_line... INFO @ Sun, 21 Jun 2020 19:36:11: start X-correlation... INFO @ Sun, 21 Jun 2020 19:36:11: end of X-cor INFO @ Sun, 21 Jun 2020 19:36:11: #2 finished! INFO @ Sun, 21 Jun 2020 19:36:11: #2 predicted fragment length is 157 bps INFO @ Sun, 21 Jun 2020 19:36:11: #2 alternative fragment length(s) may be 157 bps INFO @ Sun, 21 Jun 2020 19:36:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3011247/SRX3011247.10_model.r WARNING @ Sun, 21 Jun 2020 19:36:11: #2 Since the d (157) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:36:11: #2 You may need to consider one of the other alternative d(s): 157 WARNING @ Sun, 21 Jun 2020 19:36:11: #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 19:36:11: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:36:11: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (473 chroms): 2 millis pass2 - checking and writing primary data (6734 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:36:14: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:36:21: 9000000 INFO @ Sun, 21 Jun 2020 19:36:29: 10000000 INFO @ Sun, 21 Jun 2020 19:36:36: 11000000 INFO @ Sun, 21 Jun 2020 19:36:39: #1 tag size is determined as 80 bps INFO @ Sun, 21 Jun 2020 19:36:39: #1 tag size = 80 INFO @ Sun, 21 Jun 2020 19:36:39: #1 total tags in treatment: 11348422 INFO @ Sun, 21 Jun 2020 19:36:39: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:36:39: #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 19:36:39: #1 tags after filtering in treatment: 11348233 INFO @ Sun, 21 Jun 2020 19:36:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:36:39: #1 finished! INFO @ Sun, 21 Jun 2020 19:36:39: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:36:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:36:40: #2 number of paired peaks: 1276 INFO @ Sun, 21 Jun 2020 19:36:40: start model_add_line... INFO @ Sun, 21 Jun 2020 19:36:40: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:36:40: start X-correlation... INFO @ Sun, 21 Jun 2020 19:36:40: end of X-cor INFO @ Sun, 21 Jun 2020 19:36:40: #2 finished! INFO @ Sun, 21 Jun 2020 19:36:40: #2 predicted fragment length is 157 bps INFO @ Sun, 21 Jun 2020 19:36:40: #2 alternative fragment length(s) may be 157 bps INFO @ Sun, 21 Jun 2020 19:36:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3011247/SRX3011247.20_model.r WARNING @ Sun, 21 Jun 2020 19:36:40: #2 Since the d (157) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:36:40: #2 You may need to consider one of the other alternative d(s): 157 WARNING @ Sun, 21 Jun 2020 19:36:40: #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 19:36:40: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:36:40: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:36:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3011247/SRX3011247.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:36:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3011247/SRX3011247.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:36:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3011247/SRX3011247.10_summits.bed INFO @ Sun, 21 Jun 2020 19:36:55: Done! pass1 - making usageList (317 chroms): 1 millis pass2 - checking and writing primary data (3464 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:37:10: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:37:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3011247/SRX3011247.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:37:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3011247/SRX3011247.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:37:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3011247/SRX3011247.20_summits.bed INFO @ Sun, 21 Jun 2020 19:37:25: Done! pass1 - making usageList (169 chroms): 1 millis pass2 - checking and writing primary data (1481 records, 4 fields): 8 millis CompletedMACS2peakCalling