Job ID = 12265652 SRX = SRX7277054 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 32391233 spots for SRR10597319/SRR10597319.sra Written 32391233 spots for SRR10597319/SRR10597319.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265942 ("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: 00:30:26 32391233 reads; of these: 32391233 (100.00%) were paired; of these: 1137630 (3.51%) aligned concordantly 0 times 9863137 (30.45%) aligned concordantly exactly 1 time 21390466 (66.04%) aligned concordantly >1 times ---- 1137630 pairs aligned concordantly 0 times; of these: 230050 (20.22%) aligned discordantly 1 time ---- 907580 pairs aligned 0 times concordantly or discordantly; of these: 1815160 mates make up the pairs; of these: 918980 (50.63%) aligned 0 times 314510 (17.33%) aligned exactly 1 time 581670 (32.05%) aligned >1 times 98.58% overall alignment rate Time searching: 00:30:26 Overall time: 00:30:26 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 20 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] 18047750 / 31405759 = 0.5747 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 08:39:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7277054/SRX7277054.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7277054/SRX7277054.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7277054/SRX7277054.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7277054/SRX7277054.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 08:39:20: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:39:20: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:39:25: 1000000 INFO @ Sat, 03 Apr 2021 08:39:29: 2000000 INFO @ Sat, 03 Apr 2021 08:39:34: 3000000 INFO @ Sat, 03 Apr 2021 08:39:38: 4000000 INFO @ Sat, 03 Apr 2021 08:39:43: 5000000 INFO @ Sat, 03 Apr 2021 08:39:47: 6000000 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 08:39:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7277054/SRX7277054.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7277054/SRX7277054.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7277054/SRX7277054.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7277054/SRX7277054.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 08:39:50: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:39:50: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:39:52: 7000000 INFO @ Sat, 03 Apr 2021 08:39:55: 1000000 INFO @ Sat, 03 Apr 2021 08:39:56: 8000000 INFO @ Sat, 03 Apr 2021 08:40:00: 2000000 INFO @ Sat, 03 Apr 2021 08:40:01: 9000000 INFO @ Sat, 03 Apr 2021 08:40:06: 3000000 INFO @ Sat, 03 Apr 2021 08:40:06: 10000000 INFO @ Sat, 03 Apr 2021 08:40:10: 11000000 INFO @ Sat, 03 Apr 2021 08:40:11: 4000000 INFO @ Sat, 03 Apr 2021 08:40:15: 12000000 INFO @ Sat, 03 Apr 2021 08:40:16: 5000000 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 08:40:20: 13000000 INFO @ Sat, 03 Apr 2021 08:40:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7277054/SRX7277054.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7277054/SRX7277054.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7277054/SRX7277054.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7277054/SRX7277054.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 08:40:20: #1 read tag files... INFO @ Sat, 03 Apr 2021 08:40:20: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 08:40:21: 6000000 INFO @ Sat, 03 Apr 2021 08:40:25: 14000000 INFO @ Sat, 03 Apr 2021 08:40:25: 1000000 INFO @ Sat, 03 Apr 2021 08:40:26: 7000000 INFO @ Sat, 03 Apr 2021 08:40:29: 15000000 INFO @ Sat, 03 Apr 2021 08:40:30: 2000000 INFO @ Sat, 03 Apr 2021 08:40:31: 8000000 INFO @ Sat, 03 Apr 2021 08:40:34: 16000000 INFO @ Sat, 03 Apr 2021 08:40:35: 3000000 INFO @ Sat, 03 Apr 2021 08:40:37: 9000000 INFO @ Sat, 03 Apr 2021 08:40:39: 17000000 INFO @ Sat, 03 Apr 2021 08:40:39: 4000000 INFO @ Sat, 03 Apr 2021 08:40:42: 10000000 INFO @ Sat, 03 Apr 2021 08:40:43: 18000000 INFO @ Sat, 03 Apr 2021 08:40:44: 5000000 INFO @ Sat, 03 Apr 2021 08:40:47: 11000000 INFO @ Sat, 03 Apr 2021 08:40:48: 19000000 INFO @ Sat, 03 Apr 2021 08:40:49: 6000000 INFO @ Sat, 03 Apr 2021 08:40:52: 12000000 INFO @ Sat, 03 Apr 2021 08:40:52: 20000000 INFO @ Sat, 03 Apr 2021 08:40:54: 7000000 INFO @ Sat, 03 Apr 2021 08:40:57: 21000000 INFO @ Sat, 03 Apr 2021 08:40:57: 13000000 INFO @ Sat, 03 Apr 2021 08:40:59: 8000000 INFO @ Sat, 03 Apr 2021 08:41:02: 22000000 INFO @ Sat, 03 Apr 2021 08:41:03: 14000000 INFO @ Sat, 03 Apr 2021 08:41:04: 9000000 INFO @ Sat, 03 Apr 2021 08:41:07: 23000000 INFO @ Sat, 03 Apr 2021 08:41:08: 15000000 INFO @ Sat, 03 Apr 2021 08:41:08: 10000000 INFO @ Sat, 03 Apr 2021 08:41:11: 24000000 INFO @ Sat, 03 Apr 2021 08:41:13: 16000000 INFO @ Sat, 03 Apr 2021 08:41:13: 11000000 INFO @ Sat, 03 Apr 2021 08:41:16: 25000000 INFO @ Sat, 03 Apr 2021 08:41:18: 17000000 INFO @ Sat, 03 Apr 2021 08:41:18: 12000000 INFO @ Sat, 03 Apr 2021 08:41:21: 26000000 INFO @ Sat, 03 Apr 2021 08:41:23: 13000000 INFO @ Sat, 03 Apr 2021 08:41:23: 18000000 INFO @ Sat, 03 Apr 2021 08:41:26: 27000000 INFO @ Sat, 03 Apr 2021 08:41:28: 14000000 INFO @ Sat, 03 Apr 2021 08:41:28: 19000000 INFO @ Sat, 03 Apr 2021 08:41:29: #1 tag size is determined as 36 bps INFO @ Sat, 03 Apr 2021 08:41:29: #1 tag size = 36 INFO @ Sat, 03 Apr 2021 08:41:29: #1 total tags in treatment: 13221983 INFO @ Sat, 03 Apr 2021 08:41:29: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:41:29: #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 08:41:30: #1 tags after filtering in treatment: 9683511 INFO @ Sat, 03 Apr 2021 08:41:30: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 03 Apr 2021 08:41:30: #1 finished! INFO @ Sat, 03 Apr 2021 08:41:30: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:41:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:41:30: #2 number of paired peaks: 130 WARNING @ Sat, 03 Apr 2021 08:41:30: Fewer paired peaks (130) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 130 pairs to build model! INFO @ Sat, 03 Apr 2021 08:41:30: start model_add_line... INFO @ Sat, 03 Apr 2021 08:41:31: start X-correlation... INFO @ Sat, 03 Apr 2021 08:41:31: end of X-cor INFO @ Sat, 03 Apr 2021 08:41:31: #2 finished! INFO @ Sat, 03 Apr 2021 08:41:31: #2 predicted fragment length is 90 bps INFO @ Sat, 03 Apr 2021 08:41:31: #2 alternative fragment length(s) may be 2,41,45,90,553,594,597 bps INFO @ Sat, 03 Apr 2021 08:41:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7277054/SRX7277054.05_model.r INFO @ Sat, 03 Apr 2021 08:41:31: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:41:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:41:33: 15000000 INFO @ Sat, 03 Apr 2021 08:41:33: 20000000 INFO @ Sat, 03 Apr 2021 08:41:37: 16000000 INFO @ Sat, 03 Apr 2021 08:41:38: 21000000 INFO @ Sat, 03 Apr 2021 08:41:42: 17000000 INFO @ Sat, 03 Apr 2021 08:41:43: 22000000 INFO @ Sat, 03 Apr 2021 08:41:46: 18000000 INFO @ Sat, 03 Apr 2021 08:41:48: 23000000 INFO @ Sat, 03 Apr 2021 08:41:51: 19000000 INFO @ Sat, 03 Apr 2021 08:41:54: 24000000 INFO @ Sat, 03 Apr 2021 08:41:55: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:41:56: 20000000 INFO @ Sat, 03 Apr 2021 08:41:59: 25000000 INFO @ Sat, 03 Apr 2021 08:42:00: 21000000 INFO @ Sat, 03 Apr 2021 08:42:04: 26000000 INFO @ Sat, 03 Apr 2021 08:42:05: 22000000 INFO @ Sat, 03 Apr 2021 08:42:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7277054/SRX7277054.05_peaks.xls INFO @ Sat, 03 Apr 2021 08:42:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7277054/SRX7277054.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:42:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7277054/SRX7277054.05_summits.bed INFO @ Sat, 03 Apr 2021 08:42:07: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3174 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 08:42:09: 27000000 INFO @ Sat, 03 Apr 2021 08:42:10: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 08:42:13: #1 tag size is determined as 36 bps INFO @ Sat, 03 Apr 2021 08:42:13: #1 tag size = 36 INFO @ Sat, 03 Apr 2021 08:42:13: #1 total tags in treatment: 13221983 INFO @ Sat, 03 Apr 2021 08:42:13: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:42:13: #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 08:42:14: #1 tags after filtering in treatment: 9683511 INFO @ Sat, 03 Apr 2021 08:42:14: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 03 Apr 2021 08:42:14: #1 finished! INFO @ Sat, 03 Apr 2021 08:42:14: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:42:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:42:14: #2 number of paired peaks: 130 WARNING @ Sat, 03 Apr 2021 08:42:14: Fewer paired peaks (130) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 130 pairs to build model! INFO @ Sat, 03 Apr 2021 08:42:14: start model_add_line... INFO @ Sat, 03 Apr 2021 08:42:14: start X-correlation... INFO @ Sat, 03 Apr 2021 08:42:14: end of X-cor INFO @ Sat, 03 Apr 2021 08:42:14: #2 finished! INFO @ Sat, 03 Apr 2021 08:42:14: #2 predicted fragment length is 90 bps INFO @ Sat, 03 Apr 2021 08:42:14: #2 alternative fragment length(s) may be 2,41,45,90,553,594,597 bps INFO @ Sat, 03 Apr 2021 08:42:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7277054/SRX7277054.10_model.r INFO @ Sat, 03 Apr 2021 08:42:14: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:42:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:42:14: 24000000 INFO @ Sat, 03 Apr 2021 08:42:19: 25000000 INFO @ Sat, 03 Apr 2021 08:42:24: 26000000 INFO @ Sat, 03 Apr 2021 08:42:28: 27000000 INFO @ Sat, 03 Apr 2021 08:42:32: #1 tag size is determined as 36 bps INFO @ Sat, 03 Apr 2021 08:42:32: #1 tag size = 36 INFO @ Sat, 03 Apr 2021 08:42:32: #1 total tags in treatment: 13221983 INFO @ Sat, 03 Apr 2021 08:42:32: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:42:32: #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 08:42:32: #1 tags after filtering in treatment: 9683511 INFO @ Sat, 03 Apr 2021 08:42:32: #1 Redundant rate of treatment: 0.27 INFO @ Sat, 03 Apr 2021 08:42:32: #1 finished! INFO @ Sat, 03 Apr 2021 08:42:32: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:42:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:42:33: #2 number of paired peaks: 130 WARNING @ Sat, 03 Apr 2021 08:42:33: Fewer paired peaks (130) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 130 pairs to build model! INFO @ Sat, 03 Apr 2021 08:42:33: start model_add_line... INFO @ Sat, 03 Apr 2021 08:42:33: start X-correlation... INFO @ Sat, 03 Apr 2021 08:42:33: end of X-cor INFO @ Sat, 03 Apr 2021 08:42:33: #2 finished! INFO @ Sat, 03 Apr 2021 08:42:33: #2 predicted fragment length is 90 bps INFO @ Sat, 03 Apr 2021 08:42:33: #2 alternative fragment length(s) may be 2,41,45,90,553,594,597 bps INFO @ Sat, 03 Apr 2021 08:42:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7277054/SRX7277054.20_model.r INFO @ Sat, 03 Apr 2021 08:42:33: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:42:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:42:36: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:42:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7277054/SRX7277054.10_peaks.xls INFO @ Sat, 03 Apr 2021 08:42:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7277054/SRX7277054.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:42:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7277054/SRX7277054.10_summits.bed INFO @ Sat, 03 Apr 2021 08:42:48: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (774 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 08:42:54: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 08:43:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7277054/SRX7277054.20_peaks.xls INFO @ Sat, 03 Apr 2021 08:43:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7277054/SRX7277054.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:43:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7277054/SRX7277054.20_summits.bed INFO @ Sat, 03 Apr 2021 08:43:06: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (258 records, 4 fields): 1 millis CompletedMACS2peakCalling