Job ID = 6454536 SRX = SRX220305 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:21:29 prefetch.2.10.7: 1) Downloading 'SRR653350'... 2020-06-21T09:21:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:28:36 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:28:36 prefetch.2.10.7: 1) 'SRR653350' was downloaded successfully Read 24087614 spots for SRR653350/SRR653350.sra Written 24087614 spots for SRR653350/SRR653350.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: 00:04:56 24087614 reads; of these: 24087614 (100.00%) were unpaired; of these: 3465717 (14.39%) aligned 0 times 16480278 (68.42%) aligned exactly 1 time 4141619 (17.19%) aligned >1 times 85.61% overall alignment rate Time searching: 00:04:56 Overall time: 00:04:56 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] 6679128 / 20621897 = 0.3239 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 18:38:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX220305/SRX220305.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX220305/SRX220305.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX220305/SRX220305.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX220305/SRX220305.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 18:38:39: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:38:39: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:38:44: 1000000 INFO @ Sun, 21 Jun 2020 18:38:50: 2000000 INFO @ Sun, 21 Jun 2020 18:38:55: 3000000 INFO @ Sun, 21 Jun 2020 18:39:00: 4000000 INFO @ Sun, 21 Jun 2020 18:39:06: 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 18:39:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX220305/SRX220305.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX220305/SRX220305.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX220305/SRX220305.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX220305/SRX220305.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 18:39:09: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:39:09: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:39:11: 6000000 INFO @ Sun, 21 Jun 2020 18:39:15: 1000000 INFO @ Sun, 21 Jun 2020 18:39:17: 7000000 INFO @ Sun, 21 Jun 2020 18:39:21: 2000000 INFO @ Sun, 21 Jun 2020 18:39:23: 8000000 INFO @ Sun, 21 Jun 2020 18:39:26: 3000000 INFO @ Sun, 21 Jun 2020 18:39:29: 9000000 INFO @ Sun, 21 Jun 2020 18:39:32: 4000000 INFO @ Sun, 21 Jun 2020 18:39:35: 10000000 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 18:39:38: 5000000 INFO @ Sun, 21 Jun 2020 18:39:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX220305/SRX220305.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX220305/SRX220305.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX220305/SRX220305.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX220305/SRX220305.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 18:39:39: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:39:39: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:39:41: 11000000 INFO @ Sun, 21 Jun 2020 18:39:45: 6000000 INFO @ Sun, 21 Jun 2020 18:39:46: 1000000 INFO @ Sun, 21 Jun 2020 18:39:48: 12000000 INFO @ Sun, 21 Jun 2020 18:39:51: 7000000 INFO @ Sun, 21 Jun 2020 18:39:53: 2000000 INFO @ Sun, 21 Jun 2020 18:39:54: 13000000 INFO @ Sun, 21 Jun 2020 18:39:58: 8000000 INFO @ Sun, 21 Jun 2020 18:40:00: 3000000 INFO @ Sun, 21 Jun 2020 18:40:00: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:40:00: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:40:00: #1 total tags in treatment: 13942769 INFO @ Sun, 21 Jun 2020 18:40:00: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:40:00: #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 18:40:01: #1 tags after filtering in treatment: 13942704 INFO @ Sun, 21 Jun 2020 18:40:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:40:01: #1 finished! INFO @ Sun, 21 Jun 2020 18:40:01: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:40:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:40:02: #2 number of paired peaks: 426 WARNING @ Sun, 21 Jun 2020 18:40:02: Fewer paired peaks (426) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 426 pairs to build model! INFO @ Sun, 21 Jun 2020 18:40:02: start model_add_line... INFO @ Sun, 21 Jun 2020 18:40:02: start X-correlation... INFO @ Sun, 21 Jun 2020 18:40:02: end of X-cor INFO @ Sun, 21 Jun 2020 18:40:02: #2 finished! INFO @ Sun, 21 Jun 2020 18:40:02: #2 predicted fragment length is 109 bps INFO @ Sun, 21 Jun 2020 18:40:02: #2 alternative fragment length(s) may be 4,109 bps INFO @ Sun, 21 Jun 2020 18:40:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX220305/SRX220305.05_model.r INFO @ Sun, 21 Jun 2020 18:40:02: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:40:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:40:04: 9000000 INFO @ Sun, 21 Jun 2020 18:40:07: 4000000 INFO @ Sun, 21 Jun 2020 18:40:10: 10000000 INFO @ Sun, 21 Jun 2020 18:40:14: 5000000 INFO @ Sun, 21 Jun 2020 18:40:17: 11000000 INFO @ Sun, 21 Jun 2020 18:40:21: 6000000 INFO @ Sun, 21 Jun 2020 18:40:23: 12000000 INFO @ Sun, 21 Jun 2020 18:40:27: 7000000 INFO @ Sun, 21 Jun 2020 18:40:29: 13000000 INFO @ Sun, 21 Jun 2020 18:40:29: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:40:34: 8000000 INFO @ Sun, 21 Jun 2020 18:40:35: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:40:35: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:40:35: #1 total tags in treatment: 13942769 INFO @ Sun, 21 Jun 2020 18:40:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:40:35: #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 18:40:36: #1 tags after filtering in treatment: 13942704 INFO @ Sun, 21 Jun 2020 18:40:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:40:36: #1 finished! INFO @ Sun, 21 Jun 2020 18:40:36: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:40:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:40:37: #2 number of paired peaks: 426 WARNING @ Sun, 21 Jun 2020 18:40:37: Fewer paired peaks (426) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 426 pairs to build model! INFO @ Sun, 21 Jun 2020 18:40:37: start model_add_line... INFO @ Sun, 21 Jun 2020 18:40:37: start X-correlation... INFO @ Sun, 21 Jun 2020 18:40:37: end of X-cor INFO @ Sun, 21 Jun 2020 18:40:37: #2 finished! INFO @ Sun, 21 Jun 2020 18:40:37: #2 predicted fragment length is 109 bps INFO @ Sun, 21 Jun 2020 18:40:37: #2 alternative fragment length(s) may be 4,109 bps INFO @ Sun, 21 Jun 2020 18:40:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX220305/SRX220305.10_model.r INFO @ Sun, 21 Jun 2020 18:40:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:40:37: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:40:41: 9000000 INFO @ Sun, 21 Jun 2020 18:40:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX220305/SRX220305.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:40:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX220305/SRX220305.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:40:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX220305/SRX220305.05_summits.bed INFO @ Sun, 21 Jun 2020 18:40:43: Done! pass1 - making usageList (249 chroms): 2 millis pass2 - checking and writing primary data (7138 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:40:47: 10000000 INFO @ Sun, 21 Jun 2020 18:40:54: 11000000 INFO @ Sun, 21 Jun 2020 18:41:00: 12000000 INFO @ Sun, 21 Jun 2020 18:41:04: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:41:06: 13000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:41:12: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 18:41:12: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 18:41:12: #1 total tags in treatment: 13942769 INFO @ Sun, 21 Jun 2020 18:41:12: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:41:12: #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 18:41:13: #1 tags after filtering in treatment: 13942704 INFO @ Sun, 21 Jun 2020 18:41:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:41:13: #1 finished! INFO @ Sun, 21 Jun 2020 18:41:13: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:41:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:41:14: #2 number of paired peaks: 426 WARNING @ Sun, 21 Jun 2020 18:41:14: Fewer paired peaks (426) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 426 pairs to build model! INFO @ Sun, 21 Jun 2020 18:41:14: start model_add_line... INFO @ Sun, 21 Jun 2020 18:41:14: start X-correlation... INFO @ Sun, 21 Jun 2020 18:41:14: end of X-cor INFO @ Sun, 21 Jun 2020 18:41:14: #2 finished! INFO @ Sun, 21 Jun 2020 18:41:14: #2 predicted fragment length is 109 bps INFO @ Sun, 21 Jun 2020 18:41:14: #2 alternative fragment length(s) may be 4,109 bps INFO @ Sun, 21 Jun 2020 18:41:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX220305/SRX220305.20_model.r INFO @ Sun, 21 Jun 2020 18:41:14: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:41:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:41:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX220305/SRX220305.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:41:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX220305/SRX220305.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:41:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX220305/SRX220305.10_summits.bed INFO @ Sun, 21 Jun 2020 18:41:17: Done! pass1 - making usageList (148 chroms): 2 millis pass2 - checking and writing primary data (2720 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:41:42: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:41:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX220305/SRX220305.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:41:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX220305/SRX220305.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:41:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX220305/SRX220305.20_summits.bed INFO @ Sun, 21 Jun 2020 18:41:56: Done! pass1 - making usageList (87 chroms): 0 millis pass2 - checking and writing primary data (501 records, 4 fields): 4 millis CompletedMACS2peakCalling