Job ID = 6497690 SRX = SRX1021224 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-25T22:48:13 prefetch.2.10.7: 1) Downloading 'SRR2013421'... 2020-06-25T22:48:13 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:51:45 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:51:45 prefetch.2.10.7: 1) 'SRR2013421' was downloaded successfully Read 22783465 spots for SRR2013421/SRR2013421.sra Written 22783465 spots for SRR2013421/SRR2013421.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: 00:31:38 22783465 reads; of these: 22783465 (100.00%) were paired; of these: 7622158 (33.45%) aligned concordantly 0 times 11031522 (48.42%) aligned concordantly exactly 1 time 4129785 (18.13%) aligned concordantly >1 times ---- 7622158 pairs aligned concordantly 0 times; of these: 19294 (0.25%) aligned discordantly 1 time ---- 7602864 pairs aligned 0 times concordantly or discordantly; of these: 15205728 mates make up the pairs; of these: 14772133 (97.15%) aligned 0 times 299960 (1.97%) aligned exactly 1 time 133635 (0.88%) aligned >1 times 67.58% overall alignment rate Time searching: 00:31:38 Overall time: 00:31:38 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 16 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 2071361 / 15162175 = 0.1366 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 @ Fri, 26 Jun 2020 08:33:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1021224/SRX1021224.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1021224/SRX1021224.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1021224/SRX1021224.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1021224/SRX1021224.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 @ Fri, 26 Jun 2020 08:33:53: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:33:53: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:33:59: 1000000 INFO @ Fri, 26 Jun 2020 08:34:06: 2000000 INFO @ Fri, 26 Jun 2020 08:34:12: 3000000 INFO @ Fri, 26 Jun 2020 08:34:19: 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 @ Fri, 26 Jun 2020 08:34:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1021224/SRX1021224.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1021224/SRX1021224.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1021224/SRX1021224.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1021224/SRX1021224.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 @ Fri, 26 Jun 2020 08:34:23: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:34:23: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:34:26: 5000000 INFO @ Fri, 26 Jun 2020 08:34:30: 1000000 INFO @ Fri, 26 Jun 2020 08:34:34: 6000000 INFO @ Fri, 26 Jun 2020 08:34:38: 2000000 INFO @ Fri, 26 Jun 2020 08:34:42: 7000000 INFO @ Fri, 26 Jun 2020 08:34:45: 3000000 INFO @ Fri, 26 Jun 2020 08:34:50: 8000000 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 @ Fri, 26 Jun 2020 08:34:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1021224/SRX1021224.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1021224/SRX1021224.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1021224/SRX1021224.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1021224/SRX1021224.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 @ Fri, 26 Jun 2020 08:34:52: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:34:52: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:34:53: 4000000 INFO @ Fri, 26 Jun 2020 08:34:58: 9000000 INFO @ Fri, 26 Jun 2020 08:35:00: 1000000 INFO @ Fri, 26 Jun 2020 08:35:01: 5000000 INFO @ Fri, 26 Jun 2020 08:35:07: 10000000 INFO @ Fri, 26 Jun 2020 08:35:08: 2000000 INFO @ Fri, 26 Jun 2020 08:35:09: 6000000 INFO @ Fri, 26 Jun 2020 08:35:14: 11000000 INFO @ Fri, 26 Jun 2020 08:35:16: 3000000 INFO @ Fri, 26 Jun 2020 08:35:17: 7000000 INFO @ Fri, 26 Jun 2020 08:35:23: 12000000 INFO @ Fri, 26 Jun 2020 08:35:25: 4000000 INFO @ Fri, 26 Jun 2020 08:35:25: 8000000 INFO @ Fri, 26 Jun 2020 08:35:31: 13000000 INFO @ Fri, 26 Jun 2020 08:35:33: 5000000 INFO @ Fri, 26 Jun 2020 08:35:33: 9000000 INFO @ Fri, 26 Jun 2020 08:35:39: 14000000 INFO @ Fri, 26 Jun 2020 08:35:41: 6000000 INFO @ Fri, 26 Jun 2020 08:35:41: 10000000 INFO @ Fri, 26 Jun 2020 08:35:47: 15000000 INFO @ Fri, 26 Jun 2020 08:35:49: 7000000 INFO @ Fri, 26 Jun 2020 08:35:49: 11000000 INFO @ Fri, 26 Jun 2020 08:35:55: 16000000 INFO @ Fri, 26 Jun 2020 08:35:57: 12000000 INFO @ Fri, 26 Jun 2020 08:35:58: 8000000 INFO @ Fri, 26 Jun 2020 08:36:03: 17000000 INFO @ Fri, 26 Jun 2020 08:36:06: 9000000 INFO @ Fri, 26 Jun 2020 08:36:06: 13000000 INFO @ Fri, 26 Jun 2020 08:36:12: 18000000 INFO @ Fri, 26 Jun 2020 08:36:14: 10000000 INFO @ Fri, 26 Jun 2020 08:36:14: 14000000 INFO @ Fri, 26 Jun 2020 08:36:20: 19000000 INFO @ Fri, 26 Jun 2020 08:36:22: 11000000 INFO @ Fri, 26 Jun 2020 08:36:23: 15000000 INFO @ Fri, 26 Jun 2020 08:36:29: 20000000 INFO @ Fri, 26 Jun 2020 08:36:31: 12000000 INFO @ Fri, 26 Jun 2020 08:36:31: 16000000 INFO @ Fri, 26 Jun 2020 08:36:37: 21000000 INFO @ Fri, 26 Jun 2020 08:36:39: 13000000 INFO @ Fri, 26 Jun 2020 08:36:40: 17000000 INFO @ Fri, 26 Jun 2020 08:36:45: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 08:36:48: 14000000 INFO @ Fri, 26 Jun 2020 08:36:48: 18000000 INFO @ Fri, 26 Jun 2020 08:36:53: 23000000 INFO @ Fri, 26 Jun 2020 08:36:56: 15000000 INFO @ Fri, 26 Jun 2020 08:36:57: 19000000 INFO @ Fri, 26 Jun 2020 08:37:02: 24000000 INFO @ Fri, 26 Jun 2020 08:37:04: 16000000 INFO @ Fri, 26 Jun 2020 08:37:05: 20000000 INFO @ Fri, 26 Jun 2020 08:37:10: 25000000 INFO @ Fri, 26 Jun 2020 08:37:13: 17000000 INFO @ Fri, 26 Jun 2020 08:37:13: 21000000 INFO @ Fri, 26 Jun 2020 08:37:18: 26000000 INFO @ Fri, 26 Jun 2020 08:37:21: 18000000 INFO @ Fri, 26 Jun 2020 08:37:22: 22000000 INFO @ Fri, 26 Jun 2020 08:37:23: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:37:23: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:37:23: #1 total tags in treatment: 13091104 INFO @ Fri, 26 Jun 2020 08:37:23: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:37:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:37:24: #1 tags after filtering in treatment: 12225306 INFO @ Fri, 26 Jun 2020 08:37:24: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 26 Jun 2020 08:37:24: #1 finished! INFO @ Fri, 26 Jun 2020 08:37:24: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:37:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:37:25: #2 number of paired peaks: 398 WARNING @ Fri, 26 Jun 2020 08:37:25: Fewer paired peaks (398) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 398 pairs to build model! INFO @ Fri, 26 Jun 2020 08:37:25: start model_add_line... INFO @ Fri, 26 Jun 2020 08:37:25: start X-correlation... INFO @ Fri, 26 Jun 2020 08:37:25: end of X-cor INFO @ Fri, 26 Jun 2020 08:37:25: #2 finished! INFO @ Fri, 26 Jun 2020 08:37:25: #2 predicted fragment length is 146 bps INFO @ Fri, 26 Jun 2020 08:37:25: #2 alternative fragment length(s) may be 146 bps INFO @ Fri, 26 Jun 2020 08:37:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1021224/SRX1021224.05_model.r INFO @ Fri, 26 Jun 2020 08:37:25: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:37:25: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:37:29: 19000000 INFO @ Fri, 26 Jun 2020 08:37:29: 23000000 INFO @ Fri, 26 Jun 2020 08:37:37: 20000000 INFO @ Fri, 26 Jun 2020 08:37:38: 24000000 BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 08:37:45: 21000000 INFO @ Fri, 26 Jun 2020 08:37:45: 25000000 INFO @ Fri, 26 Jun 2020 08:37:51: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:37:53: 26000000 INFO @ Fri, 26 Jun 2020 08:37:54: 22000000 INFO @ Fri, 26 Jun 2020 08:37:59: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:37:59: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:37:59: #1 total tags in treatment: 13091104 INFO @ Fri, 26 Jun 2020 08:37:59: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:37:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:37:59: #1 tags after filtering in treatment: 12225306 INFO @ Fri, 26 Jun 2020 08:37:59: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 26 Jun 2020 08:37:59: #1 finished! INFO @ Fri, 26 Jun 2020 08:37:59: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:37:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:38:00: #2 number of paired peaks: 398 WARNING @ Fri, 26 Jun 2020 08:38:00: Fewer paired peaks (398) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 398 pairs to build model! INFO @ Fri, 26 Jun 2020 08:38:00: start model_add_line... INFO @ Fri, 26 Jun 2020 08:38:00: start X-correlation... INFO @ Fri, 26 Jun 2020 08:38:00: end of X-cor INFO @ Fri, 26 Jun 2020 08:38:00: #2 finished! INFO @ Fri, 26 Jun 2020 08:38:00: #2 predicted fragment length is 146 bps INFO @ Fri, 26 Jun 2020 08:38:00: #2 alternative fragment length(s) may be 146 bps INFO @ Fri, 26 Jun 2020 08:38:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1021224/SRX1021224.10_model.r INFO @ Fri, 26 Jun 2020 08:38:00: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:38:00: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:38:02: 23000000 INFO @ Fri, 26 Jun 2020 08:38:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1021224/SRX1021224.05_peaks.xls INFO @ Fri, 26 Jun 2020 08:38:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1021224/SRX1021224.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:38:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1021224/SRX1021224.05_summits.bed INFO @ Fri, 26 Jun 2020 08:38:06: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6841 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:38:10: 24000000 INFO @ Fri, 26 Jun 2020 08:38:17: 25000000 INFO @ Fri, 26 Jun 2020 08:38:24: 26000000 INFO @ Fri, 26 Jun 2020 08:38:29: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:38:29: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:38:29: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:38:29: #1 total tags in treatment: 13091104 INFO @ Fri, 26 Jun 2020 08:38:29: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:38:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:38:29: #1 tags after filtering in treatment: 12225306 INFO @ Fri, 26 Jun 2020 08:38:29: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 26 Jun 2020 08:38:29: #1 finished! INFO @ Fri, 26 Jun 2020 08:38:29: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:38:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:38:30: #2 number of paired peaks: 398 WARNING @ Fri, 26 Jun 2020 08:38:30: Fewer paired peaks (398) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 398 pairs to build model! INFO @ Fri, 26 Jun 2020 08:38:30: start model_add_line... INFO @ Fri, 26 Jun 2020 08:38:30: start X-correlation... INFO @ Fri, 26 Jun 2020 08:38:30: end of X-cor INFO @ Fri, 26 Jun 2020 08:38:30: #2 finished! INFO @ Fri, 26 Jun 2020 08:38:30: #2 predicted fragment length is 146 bps INFO @ Fri, 26 Jun 2020 08:38:30: #2 alternative fragment length(s) may be 146 bps INFO @ Fri, 26 Jun 2020 08:38:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1021224/SRX1021224.20_model.r INFO @ Fri, 26 Jun 2020 08:38:30: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:38:30: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:38:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1021224/SRX1021224.10_peaks.xls INFO @ Fri, 26 Jun 2020 08:38:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1021224/SRX1021224.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:38:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1021224/SRX1021224.10_summits.bed INFO @ Fri, 26 Jun 2020 08:38:44: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3830 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:38:59: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:39:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1021224/SRX1021224.20_peaks.xls INFO @ Fri, 26 Jun 2020 08:39:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1021224/SRX1021224.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:39:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1021224/SRX1021224.20_summits.bed INFO @ Fri, 26 Jun 2020 08:39:13: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1617 records, 4 fields): 7 millis CompletedMACS2peakCalling