Job ID = 6626472 SRX = SRX5736457 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 9427985 spots for SRR8956868/SRR8956868.sra Written 9427985 spots for SRR8956868/SRR8956868.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626656 ("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: 00:19:43 9427985 reads; of these: 9427985 (100.00%) were paired; of these: 2867487 (30.41%) aligned concordantly 0 times 4902642 (52.00%) aligned concordantly exactly 1 time 1657856 (17.58%) aligned concordantly >1 times ---- 2867487 pairs aligned concordantly 0 times; of these: 79231 (2.76%) aligned discordantly 1 time ---- 2788256 pairs aligned 0 times concordantly or discordantly; of these: 5576512 mates make up the pairs; of these: 5110833 (91.65%) aligned 0 times 153695 (2.76%) aligned exactly 1 time 311984 (5.59%) aligned >1 times 72.90% overall alignment rate Time searching: 00:19:43 Overall time: 00:19:44 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 8 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] 890081 / 6629015 = 0.1343 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 @ Tue, 14 Jul 2020 07:29:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736457/SRX5736457.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736457/SRX5736457.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736457/SRX5736457.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736457/SRX5736457.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 @ Tue, 14 Jul 2020 07:29:32: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:29:32: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:29:40: 1000000 INFO @ Tue, 14 Jul 2020 07:29:48: 2000000 INFO @ Tue, 14 Jul 2020 07:29:56: 3000000 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 @ Tue, 14 Jul 2020 07:30:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736457/SRX5736457.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736457/SRX5736457.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736457/SRX5736457.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736457/SRX5736457.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 @ Tue, 14 Jul 2020 07:30:02: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:30:02: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:30:04: 4000000 INFO @ Tue, 14 Jul 2020 07:30:11: 1000000 INFO @ Tue, 14 Jul 2020 07:30:13: 5000000 INFO @ Tue, 14 Jul 2020 07:30:20: 2000000 INFO @ Tue, 14 Jul 2020 07:30:22: 6000000 INFO @ Tue, 14 Jul 2020 07:30:30: 3000000 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 @ Tue, 14 Jul 2020 07:30:31: 7000000 INFO @ Tue, 14 Jul 2020 07:30:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736457/SRX5736457.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736457/SRX5736457.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736457/SRX5736457.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736457/SRX5736457.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 @ Tue, 14 Jul 2020 07:30:32: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:30:32: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:30:39: 4000000 INFO @ Tue, 14 Jul 2020 07:30:41: 8000000 INFO @ Tue, 14 Jul 2020 07:30:43: 1000000 INFO @ Tue, 14 Jul 2020 07:30:48: 5000000 INFO @ Tue, 14 Jul 2020 07:30:50: 9000000 INFO @ Tue, 14 Jul 2020 07:30:53: 2000000 INFO @ Tue, 14 Jul 2020 07:30:57: 6000000 INFO @ Tue, 14 Jul 2020 07:30:59: 10000000 INFO @ Tue, 14 Jul 2020 07:31:04: 3000000 INFO @ Tue, 14 Jul 2020 07:31:07: 7000000 INFO @ Tue, 14 Jul 2020 07:31:08: 11000000 INFO @ Tue, 14 Jul 2020 07:31:15: 4000000 INFO @ Tue, 14 Jul 2020 07:31:16: 8000000 INFO @ Tue, 14 Jul 2020 07:31:17: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 07:31:17: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 07:31:17: #1 total tags in treatment: 5676023 INFO @ Tue, 14 Jul 2020 07:31:17: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:31:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:31:17: #1 tags after filtering in treatment: 5339469 INFO @ Tue, 14 Jul 2020 07:31:17: #1 Redundant rate of treatment: 0.06 INFO @ Tue, 14 Jul 2020 07:31:17: #1 finished! INFO @ Tue, 14 Jul 2020 07:31:17: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:31:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:31:17: #2 number of paired peaks: 240 WARNING @ Tue, 14 Jul 2020 07:31:17: Fewer paired peaks (240) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 240 pairs to build model! INFO @ Tue, 14 Jul 2020 07:31:17: start model_add_line... INFO @ Tue, 14 Jul 2020 07:31:18: start X-correlation... INFO @ Tue, 14 Jul 2020 07:31:18: end of X-cor INFO @ Tue, 14 Jul 2020 07:31:18: #2 finished! INFO @ Tue, 14 Jul 2020 07:31:18: #2 predicted fragment length is 200 bps INFO @ Tue, 14 Jul 2020 07:31:18: #2 alternative fragment length(s) may be 200 bps INFO @ Tue, 14 Jul 2020 07:31:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736457/SRX5736457.05_model.r INFO @ Tue, 14 Jul 2020 07:31:18: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:31:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:31:25: 9000000 INFO @ Tue, 14 Jul 2020 07:31:26: 5000000 INFO @ Tue, 14 Jul 2020 07:31:29: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:31:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736457/SRX5736457.05_peaks.xls INFO @ Tue, 14 Jul 2020 07:31:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736457/SRX5736457.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:31:34: 10000000 INFO @ Tue, 14 Jul 2020 07:31:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736457/SRX5736457.05_summits.bed INFO @ Tue, 14 Jul 2020 07:31:35: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3136 records, 4 fields): 17 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 07:31:37: 6000000 INFO @ Tue, 14 Jul 2020 07:31:44: 11000000 INFO @ Tue, 14 Jul 2020 07:31:47: 7000000 INFO @ Tue, 14 Jul 2020 07:31:53: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 07:31:53: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 07:31:53: #1 total tags in treatment: 5676023 INFO @ Tue, 14 Jul 2020 07:31:53: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:31:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:31:53: #1 tags after filtering in treatment: 5339469 INFO @ Tue, 14 Jul 2020 07:31:53: #1 Redundant rate of treatment: 0.06 INFO @ Tue, 14 Jul 2020 07:31:53: #1 finished! INFO @ Tue, 14 Jul 2020 07:31:53: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:31:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:31:53: #2 number of paired peaks: 240 WARNING @ Tue, 14 Jul 2020 07:31:53: Fewer paired peaks (240) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 240 pairs to build model! INFO @ Tue, 14 Jul 2020 07:31:53: start model_add_line... INFO @ Tue, 14 Jul 2020 07:31:53: start X-correlation... INFO @ Tue, 14 Jul 2020 07:31:53: end of X-cor INFO @ Tue, 14 Jul 2020 07:31:53: #2 finished! INFO @ Tue, 14 Jul 2020 07:31:53: #2 predicted fragment length is 200 bps INFO @ Tue, 14 Jul 2020 07:31:53: #2 alternative fragment length(s) may be 200 bps INFO @ Tue, 14 Jul 2020 07:31:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736457/SRX5736457.10_model.r INFO @ Tue, 14 Jul 2020 07:31:53: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:31:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:31:57: 8000000 BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 07:32:04: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:32:05: 9000000 INFO @ Tue, 14 Jul 2020 07:32:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736457/SRX5736457.10_peaks.xls INFO @ Tue, 14 Jul 2020 07:32:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736457/SRX5736457.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:32:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736457/SRX5736457.10_summits.bed INFO @ Tue, 14 Jul 2020 07:32:10: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1118 records, 4 fields): 35 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:32:14: 10000000 INFO @ Tue, 14 Jul 2020 07:32:22: 11000000 INFO @ Tue, 14 Jul 2020 07:32:30: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 07:32:30: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 07:32:30: #1 total tags in treatment: 5676023 INFO @ Tue, 14 Jul 2020 07:32:30: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:32:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 07:32:30: #1 tags after filtering in treatment: 5339469 INFO @ Tue, 14 Jul 2020 07:32:30: #1 Redundant rate of treatment: 0.06 INFO @ Tue, 14 Jul 2020 07:32:30: #1 finished! INFO @ Tue, 14 Jul 2020 07:32:30: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:32:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:32:30: #2 number of paired peaks: 240 WARNING @ Tue, 14 Jul 2020 07:32:30: Fewer paired peaks (240) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 240 pairs to build model! INFO @ Tue, 14 Jul 2020 07:32:30: start model_add_line... INFO @ Tue, 14 Jul 2020 07:32:30: start X-correlation... INFO @ Tue, 14 Jul 2020 07:32:30: end of X-cor INFO @ Tue, 14 Jul 2020 07:32:30: #2 finished! INFO @ Tue, 14 Jul 2020 07:32:30: #2 predicted fragment length is 200 bps INFO @ Tue, 14 Jul 2020 07:32:30: #2 alternative fragment length(s) may be 200 bps INFO @ Tue, 14 Jul 2020 07:32:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736457/SRX5736457.20_model.r INFO @ Tue, 14 Jul 2020 07:32:30: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:32:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:32:41: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:32:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736457/SRX5736457.20_peaks.xls INFO @ Tue, 14 Jul 2020 07:32:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736457/SRX5736457.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:32:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736457/SRX5736457.20_summits.bed INFO @ Tue, 14 Jul 2020 07:32:47: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (389 records, 4 fields): 30 millis CompletedMACS2peakCalling