Job ID = 6455844 SRX = SRX3011250 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:32:06 prefetch.2.10.7: 1) Downloading 'SRR5834727'... 2020-06-21T10:32:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:35:23 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:35:24 prefetch.2.10.7: 'SRR5834727' is valid 2020-06-21T10:35:24 prefetch.2.10.7: 1) 'SRR5834727' was downloaded successfully 2020-06-21T10:36:16 prefetch.2.10.7: 'SRR5834727' has 10 unresolved dependencies 2020-06-21T10:36:16 prefetch.2.10.7: 2) Downloading 'ncbi-acc:NC_004353.3?vdb-ctx=refseq'... 2020-06-21T10:36:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:36:27 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:36:27 prefetch.2.10.7: 2) 'ncbi-acc:NC_004353.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:36:27 prefetch.2.10.7: 3) Downloading 'ncbi-acc:NC_004354.3?vdb-ctx=refseq'... 2020-06-21T10:36:27 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:36:48 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:36:48 prefetch.2.10.7: 3) 'ncbi-acc:NC_004354.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:36:48 prefetch.2.10.7: 4) Downloading 'ncbi-acc:NS_000188.1?vdb-ctx=refseq'... 2020-06-21T10:36:48 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:37:03 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:37:03 prefetch.2.10.7: 4) 'ncbi-acc:NS_000188.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:37:03 prefetch.2.10.7: 5) Downloading 'ncbi-acc:NT_033777.2?vdb-ctx=refseq'... 2020-06-21T10:37:03 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:37:21 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:37:21 prefetch.2.10.7: 5) 'ncbi-acc:NT_033777.2?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:37:21 prefetch.2.10.7: 6) Downloading 'ncbi-acc:NT_033778.3?vdb-ctx=refseq'... 2020-06-21T10:37:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:37:38 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:37:38 prefetch.2.10.7: 6) 'ncbi-acc:NT_033778.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:37:38 prefetch.2.10.7: 7) Downloading 'ncbi-acc:NT_033779.4?vdb-ctx=refseq'... 2020-06-21T10:37:38 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:37:54 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:37:54 prefetch.2.10.7: 7) 'ncbi-acc:NT_033779.4?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:37:54 prefetch.2.10.7: 8) Downloading 'ncbi-acc:NT_037436.3?vdb-ctx=refseq'... 2020-06-21T10:37:54 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:38:11 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:38:11 prefetch.2.10.7: 8) 'ncbi-acc:NT_037436.3?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:38:11 prefetch.2.10.7: 9) Downloading 'ncbi-acc:NW_001848856.1?vdb-ctx=refseq'... 2020-06-21T10:38:11 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:38:24 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:38:24 prefetch.2.10.7: 9) 'ncbi-acc:NW_001848856.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:38:24 prefetch.2.10.7: 10) Downloading 'ncbi-acc:NW_001848857.1?vdb-ctx=refseq'... 2020-06-21T10:38:24 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:38:37 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:38:37 prefetch.2.10.7: 10) 'ncbi-acc:NW_001848857.1?vdb-ctx=refseq' was downloaded successfully 2020-06-21T10:38:37 prefetch.2.10.7: 11) Downloading 'ncbi-acc:NW_001848858.1?vdb-ctx=refseq'... 2020-06-21T10:38:37 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:38:50 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:38:50 prefetch.2.10.7: 11) 'ncbi-acc:NW_001848858.1?vdb-ctx=refseq' was downloaded successfully Read 17522354 spots for SRR5834727/SRR5834727.sra Written 17522354 spots for SRR5834727/SRR5834727.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: 00:05:44 17522354 reads; of these: 17522354 (100.00%) were unpaired; of these: 288602 (1.65%) aligned 0 times 13342688 (76.15%) aligned exactly 1 time 3891064 (22.21%) aligned >1 times 98.35% overall alignment rate Time searching: 00:05:44 Overall time: 00:05:44 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] 5970920 / 17233752 = 0.3465 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 19:52:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3011250/SRX3011250.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3011250/SRX3011250.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3011250/SRX3011250.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3011250/SRX3011250.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 19:52:17: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:52:17: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:52:23: 1000000 INFO @ Sun, 21 Jun 2020 19:52:29: 2000000 INFO @ Sun, 21 Jun 2020 19:52:35: 3000000 INFO @ Sun, 21 Jun 2020 19:52:40: 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 19:52:46: 5000000 INFO @ Sun, 21 Jun 2020 19:52:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3011250/SRX3011250.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3011250/SRX3011250.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3011250/SRX3011250.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3011250/SRX3011250.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 19:52:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:52:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:52:52: 6000000 INFO @ Sun, 21 Jun 2020 19:52:54: 1000000 INFO @ Sun, 21 Jun 2020 19:52:59: 7000000 INFO @ Sun, 21 Jun 2020 19:53:00: 2000000 INFO @ Sun, 21 Jun 2020 19:53:05: 8000000 INFO @ Sun, 21 Jun 2020 19:53:07: 3000000 INFO @ Sun, 21 Jun 2020 19:53:11: 9000000 INFO @ Sun, 21 Jun 2020 19:53:13: 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 19:53:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3011250/SRX3011250.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3011250/SRX3011250.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3011250/SRX3011250.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3011250/SRX3011250.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 19:53:17: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:53:17: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:53:18: 10000000 INFO @ Sun, 21 Jun 2020 19:53:19: 5000000 INFO @ Sun, 21 Jun 2020 19:53:24: 1000000 INFO @ Sun, 21 Jun 2020 19:53:25: 11000000 INFO @ Sun, 21 Jun 2020 19:53:26: 6000000 INFO @ Sun, 21 Jun 2020 19:53:27: #1 tag size is determined as 80 bps INFO @ Sun, 21 Jun 2020 19:53:27: #1 tag size = 80 INFO @ Sun, 21 Jun 2020 19:53:27: #1 total tags in treatment: 11262832 INFO @ Sun, 21 Jun 2020 19:53:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:53:27: #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 19:53:27: #1 tags after filtering in treatment: 11262699 INFO @ Sun, 21 Jun 2020 19:53:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:53:27: #1 finished! INFO @ Sun, 21 Jun 2020 19:53:27: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:53:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:53:28: #2 number of paired peaks: 2004 INFO @ Sun, 21 Jun 2020 19:53:28: start model_add_line... INFO @ Sun, 21 Jun 2020 19:53:28: start X-correlation... INFO @ Sun, 21 Jun 2020 19:53:28: end of X-cor INFO @ Sun, 21 Jun 2020 19:53:28: #2 finished! INFO @ Sun, 21 Jun 2020 19:53:28: #2 predicted fragment length is 144 bps INFO @ Sun, 21 Jun 2020 19:53:28: #2 alternative fragment length(s) may be 144 bps INFO @ Sun, 21 Jun 2020 19:53:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3011250/SRX3011250.05_model.r WARNING @ Sun, 21 Jun 2020 19:53:30: #2 Since the d (144) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:53:30: #2 You may need to consider one of the other alternative d(s): 144 WARNING @ Sun, 21 Jun 2020 19:53:30: #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 19:53:30: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:53:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:53:31: 2000000 INFO @ Sun, 21 Jun 2020 19:53:32: 7000000 INFO @ Sun, 21 Jun 2020 19:53:37: 8000000 INFO @ Sun, 21 Jun 2020 19:53:38: 3000000 INFO @ Sun, 21 Jun 2020 19:53:44: 9000000 INFO @ Sun, 21 Jun 2020 19:53:44: 4000000 INFO @ Sun, 21 Jun 2020 19:53:51: 10000000 INFO @ Sun, 21 Jun 2020 19:53:51: 5000000 INFO @ Sun, 21 Jun 2020 19:53:57: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:53:57: 11000000 INFO @ Sun, 21 Jun 2020 19:53:58: 6000000 INFO @ Sun, 21 Jun 2020 19:54:00: #1 tag size is determined as 80 bps INFO @ Sun, 21 Jun 2020 19:54:00: #1 tag size = 80 INFO @ Sun, 21 Jun 2020 19:54:00: #1 total tags in treatment: 11262832 INFO @ Sun, 21 Jun 2020 19:54:00: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:54:00: #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 19:54:00: #1 tags after filtering in treatment: 11262699 INFO @ Sun, 21 Jun 2020 19:54:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:54:00: #1 finished! INFO @ Sun, 21 Jun 2020 19:54:00: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:54:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:54:01: #2 number of paired peaks: 2004 INFO @ Sun, 21 Jun 2020 19:54:01: start model_add_line... INFO @ Sun, 21 Jun 2020 19:54:01: start X-correlation... INFO @ Sun, 21 Jun 2020 19:54:01: end of X-cor INFO @ Sun, 21 Jun 2020 19:54:01: #2 finished! INFO @ Sun, 21 Jun 2020 19:54:01: #2 predicted fragment length is 144 bps INFO @ Sun, 21 Jun 2020 19:54:01: #2 alternative fragment length(s) may be 144 bps INFO @ Sun, 21 Jun 2020 19:54:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3011250/SRX3011250.10_model.r WARNING @ Sun, 21 Jun 2020 19:54:01: #2 Since the d (144) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:54:01: #2 You may need to consider one of the other alternative d(s): 144 WARNING @ Sun, 21 Jun 2020 19:54:01: #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 19:54:01: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:54:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:54:04: 7000000 INFO @ Sun, 21 Jun 2020 19:54:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3011250/SRX3011250.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:54:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3011250/SRX3011250.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:54:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3011250/SRX3011250.05_summits.bed INFO @ Sun, 21 Jun 2020 19:54:10: Done! pass1 - making usageList (362 chroms): 3 millis pass2 - checking and writing primary data (9377 records, 4 fields): 30 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:54:11: 8000000 INFO @ Sun, 21 Jun 2020 19:54:18: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:54:27: 10000000 INFO @ Sun, 21 Jun 2020 19:54:28: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:54:34: 11000000 INFO @ Sun, 21 Jun 2020 19:54:37: #1 tag size is determined as 80 bps INFO @ Sun, 21 Jun 2020 19:54:37: #1 tag size = 80 INFO @ Sun, 21 Jun 2020 19:54:37: #1 total tags in treatment: 11262832 INFO @ Sun, 21 Jun 2020 19:54:37: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:54:37: #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 19:54:37: #1 tags after filtering in treatment: 11262699 INFO @ Sun, 21 Jun 2020 19:54:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:54:37: #1 finished! INFO @ Sun, 21 Jun 2020 19:54:37: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:54:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:54:38: #2 number of paired peaks: 2004 INFO @ Sun, 21 Jun 2020 19:54:38: start model_add_line... INFO @ Sun, 21 Jun 2020 19:54:38: start X-correlation... INFO @ Sun, 21 Jun 2020 19:54:38: end of X-cor INFO @ Sun, 21 Jun 2020 19:54:38: #2 finished! INFO @ Sun, 21 Jun 2020 19:54:38: #2 predicted fragment length is 144 bps INFO @ Sun, 21 Jun 2020 19:54:38: #2 alternative fragment length(s) may be 144 bps INFO @ Sun, 21 Jun 2020 19:54:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3011250/SRX3011250.20_model.r WARNING @ Sun, 21 Jun 2020 19:54:38: #2 Since the d (144) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:54:38: #2 You may need to consider one of the other alternative d(s): 144 WARNING @ Sun, 21 Jun 2020 19:54:38: #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 19:54:38: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:54:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:54:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3011250/SRX3011250.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:54:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3011250/SRX3011250.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:54:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3011250/SRX3011250.10_summits.bed INFO @ Sun, 21 Jun 2020 19:54:41: Done! pass1 - making usageList (264 chroms): 1 millis pass2 - checking and writing primary data (5743 records, 4 fields): 22 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:55:06: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:55:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3011250/SRX3011250.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:55:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3011250/SRX3011250.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:55:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3011250/SRX3011250.20_summits.bed INFO @ Sun, 21 Jun 2020 19:55:19: Done! pass1 - making usageList (195 chroms): 1 millis pass2 - checking and writing primary data (2504 records, 4 fields): 14 millis CompletedMACS2peakCalling