Job ID = 12265650 SRX = SRX7277052 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 44382858 spots for SRR10597317/SRR10597317.sra Written 44382858 spots for SRR10597317/SRR10597317.sra fastq に変換しました。 bowtie でマッピング中... Your job 12266220 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:48:27 44382858 reads; of these: 44382858 (100.00%) were paired; of these: 1494921 (3.37%) aligned concordantly 0 times 10859393 (24.47%) aligned concordantly exactly 1 time 32028544 (72.16%) aligned concordantly >1 times ---- 1494921 pairs aligned concordantly 0 times; of these: 269710 (18.04%) aligned discordantly 1 time ---- 1225211 pairs aligned 0 times concordantly or discordantly; of these: 2450422 mates make up the pairs; of these: 1192348 (48.66%) aligned 0 times 373725 (15.25%) aligned exactly 1 time 884349 (36.09%) aligned >1 times 98.66% overall alignment rate Time searching: 00:48:27 Overall time: 00:48:27 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 24 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] 29068034 / 43063160 = 0.6750 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 09:01:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7277052/SRX7277052.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7277052/SRX7277052.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7277052/SRX7277052.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7277052/SRX7277052.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 @ Sat, 03 Apr 2021 09:01:19: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:01:19: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:01:26: 1000000 INFO @ Sat, 03 Apr 2021 09:01:33: 2000000 INFO @ Sat, 03 Apr 2021 09:01:39: 3000000 INFO @ Sat, 03 Apr 2021 09:01:46: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 09:01:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7277052/SRX7277052.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7277052/SRX7277052.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7277052/SRX7277052.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7277052/SRX7277052.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 @ Sat, 03 Apr 2021 09:01:50: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:01:50: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:01:53: 5000000 INFO @ Sat, 03 Apr 2021 09:01:57: 1000000 INFO @ Sat, 03 Apr 2021 09:02:00: 6000000 INFO @ Sat, 03 Apr 2021 09:02:05: 2000000 INFO @ Sat, 03 Apr 2021 09:02:08: 7000000 INFO @ Sat, 03 Apr 2021 09:02:12: 3000000 INFO @ Sat, 03 Apr 2021 09:02:15: 8000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 09:02:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7277052/SRX7277052.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7277052/SRX7277052.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7277052/SRX7277052.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7277052/SRX7277052.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 @ Sat, 03 Apr 2021 09:02:19: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:02:19: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:02:20: 4000000 INFO @ Sat, 03 Apr 2021 09:02:22: 9000000 INFO @ Sat, 03 Apr 2021 09:02:27: 1000000 INFO @ Sat, 03 Apr 2021 09:02:27: 5000000 INFO @ Sat, 03 Apr 2021 09:02:30: 10000000 INFO @ Sat, 03 Apr 2021 09:02:34: 2000000 INFO @ Sat, 03 Apr 2021 09:02:35: 6000000 INFO @ Sat, 03 Apr 2021 09:02:37: 11000000 INFO @ Sat, 03 Apr 2021 09:02:41: 3000000 INFO @ Sat, 03 Apr 2021 09:02:43: 7000000 INFO @ Sat, 03 Apr 2021 09:02:45: 12000000 INFO @ Sat, 03 Apr 2021 09:02:48: 4000000 INFO @ Sat, 03 Apr 2021 09:02:50: 8000000 INFO @ Sat, 03 Apr 2021 09:02:53: 13000000 INFO @ Sat, 03 Apr 2021 09:02:56: 5000000 INFO @ Sat, 03 Apr 2021 09:02:58: 9000000 INFO @ Sat, 03 Apr 2021 09:03:01: 14000000 INFO @ Sat, 03 Apr 2021 09:03:03: 6000000 INFO @ Sat, 03 Apr 2021 09:03:06: 10000000 INFO @ Sat, 03 Apr 2021 09:03:08: 15000000 INFO @ Sat, 03 Apr 2021 09:03:10: 7000000 INFO @ Sat, 03 Apr 2021 09:03:13: 11000000 INFO @ Sat, 03 Apr 2021 09:03:16: 16000000 INFO @ Sat, 03 Apr 2021 09:03:18: 8000000 INFO @ Sat, 03 Apr 2021 09:03:21: 12000000 INFO @ Sat, 03 Apr 2021 09:03:23: 17000000 INFO @ Sat, 03 Apr 2021 09:03:25: 9000000 INFO @ Sat, 03 Apr 2021 09:03:28: 13000000 INFO @ Sat, 03 Apr 2021 09:03:30: 18000000 INFO @ Sat, 03 Apr 2021 09:03:33: 10000000 INFO @ Sat, 03 Apr 2021 09:03:35: 14000000 INFO @ Sat, 03 Apr 2021 09:03:38: 19000000 INFO @ Sat, 03 Apr 2021 09:03:40: 11000000 INFO @ Sat, 03 Apr 2021 09:03:43: 15000000 INFO @ Sat, 03 Apr 2021 09:03:45: 20000000 INFO @ Sat, 03 Apr 2021 09:03:47: 12000000 INFO @ Sat, 03 Apr 2021 09:03:51: 16000000 INFO @ Sat, 03 Apr 2021 09:03:53: 21000000 INFO @ Sat, 03 Apr 2021 09:03:54: 13000000 INFO @ Sat, 03 Apr 2021 09:03:58: 17000000 INFO @ Sat, 03 Apr 2021 09:04:00: 22000000 INFO @ Sat, 03 Apr 2021 09:04:02: 14000000 INFO @ Sat, 03 Apr 2021 09:04:05: 18000000 INFO @ Sat, 03 Apr 2021 09:04:07: 23000000 INFO @ Sat, 03 Apr 2021 09:04:09: 15000000 INFO @ Sat, 03 Apr 2021 09:04:13: 19000000 INFO @ Sat, 03 Apr 2021 09:04:15: 24000000 INFO @ Sat, 03 Apr 2021 09:04:16: 16000000 INFO @ Sat, 03 Apr 2021 09:04:20: 20000000 INFO @ Sat, 03 Apr 2021 09:04:22: 25000000 INFO @ Sat, 03 Apr 2021 09:04:23: 17000000 INFO @ Sat, 03 Apr 2021 09:04:27: 21000000 INFO @ Sat, 03 Apr 2021 09:04:30: 26000000 INFO @ Sat, 03 Apr 2021 09:04:30: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 09:04:35: 22000000 INFO @ Sat, 03 Apr 2021 09:04:37: 19000000 INFO @ Sat, 03 Apr 2021 09:04:38: 27000000 INFO @ Sat, 03 Apr 2021 09:04:42: 23000000 INFO @ Sat, 03 Apr 2021 09:04:44: 20000000 INFO @ Sat, 03 Apr 2021 09:04:45: 28000000 INFO @ Sat, 03 Apr 2021 09:04:50: 24000000 INFO @ Sat, 03 Apr 2021 09:04:51: 21000000 INFO @ Sat, 03 Apr 2021 09:04:52: 29000000 INFO @ Sat, 03 Apr 2021 09:04:56: #1 tag size is determined as 36 bps INFO @ Sat, 03 Apr 2021 09:04:56: #1 tag size = 36 INFO @ Sat, 03 Apr 2021 09:04:56: #1 total tags in treatment: 13857144 INFO @ Sat, 03 Apr 2021 09:04:56: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:04:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 09:04:56: #1 tags after filtering in treatment: 9831805 INFO @ Sat, 03 Apr 2021 09:04:56: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 03 Apr 2021 09:04:56: #1 finished! INFO @ Sat, 03 Apr 2021 09:04:56: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:04:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 09:04:57: #2 number of paired peaks: 193 WARNING @ Sat, 03 Apr 2021 09:04:57: Fewer paired peaks (193) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 193 pairs to build model! INFO @ Sat, 03 Apr 2021 09:04:57: start model_add_line... INFO @ Sat, 03 Apr 2021 09:04:57: start X-correlation... INFO @ Sat, 03 Apr 2021 09:04:57: end of X-cor INFO @ Sat, 03 Apr 2021 09:04:57: #2 finished! INFO @ Sat, 03 Apr 2021 09:04:57: #2 predicted fragment length is 95 bps INFO @ Sat, 03 Apr 2021 09:04:57: #2 alternative fragment length(s) may be 4,95 bps INFO @ Sat, 03 Apr 2021 09:04:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7277052/SRX7277052.05_model.r INFO @ Sat, 03 Apr 2021 09:04:57: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:04:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 09:04:57: 25000000 INFO @ Sat, 03 Apr 2021 09:04:58: 22000000 INFO @ Sat, 03 Apr 2021 09:05:05: 26000000 INFO @ Sat, 03 Apr 2021 09:05:05: 23000000 INFO @ Sat, 03 Apr 2021 09:05:12: 27000000 INFO @ Sat, 03 Apr 2021 09:05:12: 24000000 BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 09:05:19: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 09:05:20: 25000000 INFO @ Sat, 03 Apr 2021 09:05:20: 28000000 INFO @ Sat, 03 Apr 2021 09:05:27: 26000000 INFO @ Sat, 03 Apr 2021 09:05:27: 29000000 INFO @ Sat, 03 Apr 2021 09:05:30: #1 tag size is determined as 36 bps INFO @ Sat, 03 Apr 2021 09:05:30: #1 tag size = 36 INFO @ Sat, 03 Apr 2021 09:05:30: #1 total tags in treatment: 13857144 INFO @ Sat, 03 Apr 2021 09:05:30: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:05:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 09:05:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7277052/SRX7277052.05_peaks.xls INFO @ Sat, 03 Apr 2021 09:05:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7277052/SRX7277052.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:05:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7277052/SRX7277052.05_summits.bed INFO @ Sat, 03 Apr 2021 09:05:31: Done! INFO @ Sat, 03 Apr 2021 09:05:31: #1 tags after filtering in treatment: 9831805 INFO @ Sat, 03 Apr 2021 09:05:31: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 03 Apr 2021 09:05:31: #1 finished! INFO @ Sat, 03 Apr 2021 09:05:31: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:05:31: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3308 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 09:05:31: #2 number of paired peaks: 193 WARNING @ Sat, 03 Apr 2021 09:05:31: Fewer paired peaks (193) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 193 pairs to build model! INFO @ Sat, 03 Apr 2021 09:05:31: start model_add_line... INFO @ Sat, 03 Apr 2021 09:05:31: start X-correlation... INFO @ Sat, 03 Apr 2021 09:05:31: end of X-cor INFO @ Sat, 03 Apr 2021 09:05:31: #2 finished! INFO @ Sat, 03 Apr 2021 09:05:31: #2 predicted fragment length is 95 bps INFO @ Sat, 03 Apr 2021 09:05:31: #2 alternative fragment length(s) may be 4,95 bps INFO @ Sat, 03 Apr 2021 09:05:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7277052/SRX7277052.10_model.r INFO @ Sat, 03 Apr 2021 09:05:31: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:05:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 09:05:33: 27000000 INFO @ Sat, 03 Apr 2021 09:05:40: 28000000 INFO @ Sat, 03 Apr 2021 09:05:46: 29000000 INFO @ Sat, 03 Apr 2021 09:05:48: #1 tag size is determined as 36 bps INFO @ Sat, 03 Apr 2021 09:05:48: #1 tag size = 36 INFO @ Sat, 03 Apr 2021 09:05:48: #1 total tags in treatment: 13857144 INFO @ Sat, 03 Apr 2021 09:05:48: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:05:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 09:05:48: #1 tags after filtering in treatment: 9831805 INFO @ Sat, 03 Apr 2021 09:05:48: #1 Redundant rate of treatment: 0.29 INFO @ Sat, 03 Apr 2021 09:05:48: #1 finished! INFO @ Sat, 03 Apr 2021 09:05:48: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:05:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 09:05:49: #2 number of paired peaks: 193 WARNING @ Sat, 03 Apr 2021 09:05:49: Fewer paired peaks (193) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 193 pairs to build model! INFO @ Sat, 03 Apr 2021 09:05:49: start model_add_line... INFO @ Sat, 03 Apr 2021 09:05:49: start X-correlation... INFO @ Sat, 03 Apr 2021 09:05:49: end of X-cor INFO @ Sat, 03 Apr 2021 09:05:49: #2 finished! INFO @ Sat, 03 Apr 2021 09:05:49: #2 predicted fragment length is 95 bps INFO @ Sat, 03 Apr 2021 09:05:49: #2 alternative fragment length(s) may be 4,95 bps INFO @ Sat, 03 Apr 2021 09:05:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7277052/SRX7277052.20_model.r INFO @ Sat, 03 Apr 2021 09:05:49: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:05:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 09:05:53: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 09:06:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7277052/SRX7277052.10_peaks.xls INFO @ Sat, 03 Apr 2021 09:06:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7277052/SRX7277052.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:06:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7277052/SRX7277052.10_summits.bed INFO @ Sat, 03 Apr 2021 09:06:04: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1117 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 09:06:12: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 09:06:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7277052/SRX7277052.20_peaks.xls INFO @ Sat, 03 Apr 2021 09:06:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7277052/SRX7277052.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:06:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7277052/SRX7277052.20_summits.bed INFO @ Sat, 03 Apr 2021 09:06:24: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (508 records, 4 fields): 1 millis CompletedMACS2peakCalling