Job ID = 6459850 SRX = SRX886167 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:35:58 prefetch.2.10.7: 1) Downloading 'SRR1813781'... 2020-06-21T13:35:58 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:38:44 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:38:44 prefetch.2.10.7: 1) 'SRR1813781' was downloaded successfully Read 19021504 spots for SRR1813781/SRR1813781.sra Written 19021504 spots for SRR1813781/SRR1813781.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: 00:04:47 19021504 reads; of these: 19021504 (100.00%) were unpaired; of these: 908172 (4.77%) aligned 0 times 13182923 (69.31%) aligned exactly 1 time 4930409 (25.92%) aligned >1 times 95.23% overall alignment rate Time searching: 00:04:47 Overall time: 00:04:47 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] 7466328 / 18113332 = 0.4122 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 22:48:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX886167/SRX886167.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX886167/SRX886167.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX886167/SRX886167.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX886167/SRX886167.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 22:48:51: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:48:51: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:48:57: 1000000 INFO @ Sun, 21 Jun 2020 22:49:03: 2000000 INFO @ Sun, 21 Jun 2020 22:49:09: 3000000 INFO @ Sun, 21 Jun 2020 22:49:15: 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 22:49:21: 5000000 INFO @ Sun, 21 Jun 2020 22:49:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX886167/SRX886167.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX886167/SRX886167.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX886167/SRX886167.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX886167/SRX886167.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 22:49:21: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:49:21: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:49:28: 6000000 INFO @ Sun, 21 Jun 2020 22:49:29: 1000000 INFO @ Sun, 21 Jun 2020 22:49:35: 7000000 INFO @ Sun, 21 Jun 2020 22:49:37: 2000000 INFO @ Sun, 21 Jun 2020 22:49:41: 8000000 INFO @ Sun, 21 Jun 2020 22:49:45: 3000000 INFO @ Sun, 21 Jun 2020 22:49:49: 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 22:49:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX886167/SRX886167.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX886167/SRX886167.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX886167/SRX886167.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX886167/SRX886167.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 22:49:51: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:49:51: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:49:53: 4000000 INFO @ Sun, 21 Jun 2020 22:49:56: 10000000 INFO @ Sun, 21 Jun 2020 22:49:59: 1000000 INFO @ Sun, 21 Jun 2020 22:50:01: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:50:01: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:50:01: #1 total tags in treatment: 10647004 INFO @ Sun, 21 Jun 2020 22:50:01: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:50:01: #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 22:50:01: #1 tags after filtering in treatment: 10646894 INFO @ Sun, 21 Jun 2020 22:50:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:50:01: #1 finished! INFO @ Sun, 21 Jun 2020 22:50:01: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:50:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:50:01: 5000000 INFO @ Sun, 21 Jun 2020 22:50:02: #2 number of paired peaks: 2236 INFO @ Sun, 21 Jun 2020 22:50:02: start model_add_line... INFO @ Sun, 21 Jun 2020 22:50:02: start X-correlation... INFO @ Sun, 21 Jun 2020 22:50:02: end of X-cor INFO @ Sun, 21 Jun 2020 22:50:02: #2 finished! INFO @ Sun, 21 Jun 2020 22:50:02: #2 predicted fragment length is 52 bps INFO @ Sun, 21 Jun 2020 22:50:02: #2 alternative fragment length(s) may be 2,52 bps INFO @ Sun, 21 Jun 2020 22:50:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX886167/SRX886167.05_model.r WARNING @ Sun, 21 Jun 2020 22:50:02: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:50:02: #2 You may need to consider one of the other alternative d(s): 2,52 WARNING @ Sun, 21 Jun 2020 22:50:02: #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 22:50:02: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:50:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:50:06: 2000000 INFO @ Sun, 21 Jun 2020 22:50:09: 6000000 INFO @ Sun, 21 Jun 2020 22:50:13: 3000000 INFO @ Sun, 21 Jun 2020 22:50:17: 7000000 INFO @ Sun, 21 Jun 2020 22:50:20: 4000000 INFO @ Sun, 21 Jun 2020 22:50:25: 8000000 INFO @ Sun, 21 Jun 2020 22:50:27: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:50:27: 5000000 INFO @ Sun, 21 Jun 2020 22:50:33: 9000000 INFO @ Sun, 21 Jun 2020 22:50:34: 6000000 INFO @ Sun, 21 Jun 2020 22:50:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX886167/SRX886167.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:50:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX886167/SRX886167.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:50:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX886167/SRX886167.05_summits.bed INFO @ Sun, 21 Jun 2020 22:50:39: Done! pass1 - making usageList (529 chroms): 1 millis pass2 - checking and writing primary data (2565 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:50:41: 10000000 INFO @ Sun, 21 Jun 2020 22:50:41: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:50:46: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:50:46: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:50:46: #1 total tags in treatment: 10647004 INFO @ Sun, 21 Jun 2020 22:50:46: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:50:46: #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 22:50:47: #1 tags after filtering in treatment: 10646894 INFO @ Sun, 21 Jun 2020 22:50:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:50:47: #1 finished! INFO @ Sun, 21 Jun 2020 22:50:47: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:50:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:50:48: #2 number of paired peaks: 2236 INFO @ Sun, 21 Jun 2020 22:50:48: start model_add_line... INFO @ Sun, 21 Jun 2020 22:50:48: start X-correlation... INFO @ Sun, 21 Jun 2020 22:50:48: end of X-cor INFO @ Sun, 21 Jun 2020 22:50:48: #2 finished! INFO @ Sun, 21 Jun 2020 22:50:48: #2 predicted fragment length is 52 bps INFO @ Sun, 21 Jun 2020 22:50:48: #2 alternative fragment length(s) may be 2,52 bps INFO @ Sun, 21 Jun 2020 22:50:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX886167/SRX886167.10_model.r WARNING @ Sun, 21 Jun 2020 22:50:48: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:50:48: #2 You may need to consider one of the other alternative d(s): 2,52 WARNING @ Sun, 21 Jun 2020 22:50:48: #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 22:50:48: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:50:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:50:48: 8000000 INFO @ Sun, 21 Jun 2020 22:50:55: 9000000 INFO @ Sun, 21 Jun 2020 22:51:01: 10000000 INFO @ Sun, 21 Jun 2020 22:51:05: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:51:05: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:51:05: #1 total tags in treatment: 10647004 INFO @ Sun, 21 Jun 2020 22:51:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:51:05: #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 22:51:06: #1 tags after filtering in treatment: 10646894 INFO @ Sun, 21 Jun 2020 22:51:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:51:06: #1 finished! INFO @ Sun, 21 Jun 2020 22:51:06: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:51:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:51:07: #2 number of paired peaks: 2236 INFO @ Sun, 21 Jun 2020 22:51:07: start model_add_line... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:51:07: start X-correlation... INFO @ Sun, 21 Jun 2020 22:51:07: end of X-cor INFO @ Sun, 21 Jun 2020 22:51:07: #2 finished! INFO @ Sun, 21 Jun 2020 22:51:07: #2 predicted fragment length is 52 bps INFO @ Sun, 21 Jun 2020 22:51:07: #2 alternative fragment length(s) may be 2,52 bps INFO @ Sun, 21 Jun 2020 22:51:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX886167/SRX886167.20_model.r WARNING @ Sun, 21 Jun 2020 22:51:07: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:51:07: #2 You may need to consider one of the other alternative d(s): 2,52 WARNING @ Sun, 21 Jun 2020 22:51:07: #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 22:51:07: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:51:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:51:12: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:51:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX886167/SRX886167.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:51:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX886167/SRX886167.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:51:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX886167/SRX886167.10_summits.bed INFO @ Sun, 21 Jun 2020 22:51:25: Done! pass1 - making usageList (267 chroms): 1 millis pass2 - checking and writing primary data (999 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:51:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:51:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX886167/SRX886167.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:51:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX886167/SRX886167.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:51:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX886167/SRX886167.20_summits.bed INFO @ Sun, 21 Jun 2020 22:51:44: Done! pass1 - making usageList (149 chroms): 0 millis pass2 - checking and writing primary data (440 records, 4 fields): 6 millis CompletedMACS2peakCalling