Job ID = 6626487 SRX = SRX5736468 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 5917319 spots for SRR8956880/SRR8956880.sra Written 5917319 spots for SRR8956880/SRR8956880.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626657 ("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: 00:17:48 5917319 reads; of these: 5917319 (100.00%) were paired; of these: 1633835 (27.61%) aligned concordantly 0 times 2930634 (49.53%) aligned concordantly exactly 1 time 1352850 (22.86%) aligned concordantly >1 times ---- 1633835 pairs aligned concordantly 0 times; of these: 96509 (5.91%) aligned discordantly 1 time ---- 1537326 pairs aligned 0 times concordantly or discordantly; of these: 3074652 mates make up the pairs; of these: 2679301 (87.14%) aligned 0 times 118347 (3.85%) aligned exactly 1 time 277004 (9.01%) aligned >1 times 77.36% overall alignment rate Time searching: 00:17:48 Overall time: 00:17:48 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_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] 784143 / 4371770 = 0.1794 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 07:28:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736468/SRX5736468.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736468/SRX5736468.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736468/SRX5736468.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736468/SRX5736468.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 07:28:26: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:28:26: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:28:33: 1000000 INFO @ Tue, 14 Jul 2020 07:28:40: 2000000 INFO @ Tue, 14 Jul 2020 07:28:46: 3000000 INFO @ Tue, 14 Jul 2020 07:28:53: 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 @ Tue, 14 Jul 2020 07:28:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736468/SRX5736468.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736468/SRX5736468.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736468/SRX5736468.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736468/SRX5736468.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 07:28:56: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:28:56: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:29:01: 5000000 INFO @ Tue, 14 Jul 2020 07:29:04: 1000000 INFO @ Tue, 14 Jul 2020 07:29:08: 6000000 INFO @ Tue, 14 Jul 2020 07:29:12: 2000000 INFO @ Tue, 14 Jul 2020 07:29:16: 7000000 INFO @ Tue, 14 Jul 2020 07:29:20: 3000000 INFO @ Tue, 14 Jul 2020 07:29:21: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 07:29:21: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 07:29:21: #1 total tags in treatment: 3506924 INFO @ Tue, 14 Jul 2020 07:29:21: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:29:21: #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 07:29:21: #1 tags after filtering in treatment: 3364021 INFO @ Tue, 14 Jul 2020 07:29:21: #1 Redundant rate of treatment: 0.04 INFO @ Tue, 14 Jul 2020 07:29:21: #1 finished! INFO @ Tue, 14 Jul 2020 07:29:21: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:29:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:29:21: #2 number of paired peaks: 535 WARNING @ Tue, 14 Jul 2020 07:29:21: Fewer paired peaks (535) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 535 pairs to build model! INFO @ Tue, 14 Jul 2020 07:29:21: start model_add_line... INFO @ Tue, 14 Jul 2020 07:29:21: start X-correlation... INFO @ Tue, 14 Jul 2020 07:29:21: end of X-cor INFO @ Tue, 14 Jul 2020 07:29:21: #2 finished! INFO @ Tue, 14 Jul 2020 07:29:21: #2 predicted fragment length is 226 bps INFO @ Tue, 14 Jul 2020 07:29:21: #2 alternative fragment length(s) may be 226 bps INFO @ Tue, 14 Jul 2020 07:29:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736468/SRX5736468.05_model.r INFO @ Tue, 14 Jul 2020 07:29:21: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:29:21: #3 Pre-compute pvalue-qvalue table... 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 07:29:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5736468/SRX5736468.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5736468/SRX5736468.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5736468/SRX5736468.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5736468/SRX5736468.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 07:29:26: #1 read tag files... INFO @ Tue, 14 Jul 2020 07:29:26: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 07:29:28: 4000000 INFO @ Tue, 14 Jul 2020 07:29:29: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:29:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736468/SRX5736468.05_peaks.xls INFO @ Tue, 14 Jul 2020 07:29:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736468/SRX5736468.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:29:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736468/SRX5736468.05_summits.bed INFO @ Tue, 14 Jul 2020 07:29:34: Done! INFO @ Tue, 14 Jul 2020 07:29:34: 1000000 pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2608 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:29:36: 5000000 INFO @ Tue, 14 Jul 2020 07:29:42: 2000000 INFO @ Tue, 14 Jul 2020 07:29:44: 6000000 INFO @ Tue, 14 Jul 2020 07:29:50: 3000000 INFO @ Tue, 14 Jul 2020 07:29:52: 7000000 INFO @ Tue, 14 Jul 2020 07:29:56: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 07:29:56: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 07:29:56: #1 total tags in treatment: 3506924 INFO @ Tue, 14 Jul 2020 07:29:56: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:29:56: #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 07:29:57: #1 tags after filtering in treatment: 3364021 INFO @ Tue, 14 Jul 2020 07:29:57: #1 Redundant rate of treatment: 0.04 INFO @ Tue, 14 Jul 2020 07:29:57: #1 finished! INFO @ Tue, 14 Jul 2020 07:29:57: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:29:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:29:57: #2 number of paired peaks: 535 WARNING @ Tue, 14 Jul 2020 07:29:57: Fewer paired peaks (535) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 535 pairs to build model! INFO @ Tue, 14 Jul 2020 07:29:57: start model_add_line... INFO @ Tue, 14 Jul 2020 07:29:57: start X-correlation... INFO @ Tue, 14 Jul 2020 07:29:57: end of X-cor INFO @ Tue, 14 Jul 2020 07:29:57: #2 finished! INFO @ Tue, 14 Jul 2020 07:29:57: #2 predicted fragment length is 226 bps INFO @ Tue, 14 Jul 2020 07:29:57: #2 alternative fragment length(s) may be 226 bps INFO @ Tue, 14 Jul 2020 07:29:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736468/SRX5736468.10_model.r INFO @ Tue, 14 Jul 2020 07:29:57: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:29:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:29:58: 4000000 INFO @ Tue, 14 Jul 2020 07:30:05: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 07:30:06: 5000000 INFO @ Tue, 14 Jul 2020 07:30:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736468/SRX5736468.10_peaks.xls INFO @ Tue, 14 Jul 2020 07:30:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736468/SRX5736468.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:30:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736468/SRX5736468.10_summits.bed INFO @ Tue, 14 Jul 2020 07:30:10: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1067 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 07:30:13: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 07:30:20: 7000000 INFO @ Tue, 14 Jul 2020 07:30:24: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 07:30:24: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 07:30:24: #1 total tags in treatment: 3506924 INFO @ Tue, 14 Jul 2020 07:30:24: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 07:30:24: #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 07:30:25: #1 tags after filtering in treatment: 3364021 INFO @ Tue, 14 Jul 2020 07:30:25: #1 Redundant rate of treatment: 0.04 INFO @ Tue, 14 Jul 2020 07:30:25: #1 finished! INFO @ Tue, 14 Jul 2020 07:30:25: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 07:30:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 07:30:25: #2 number of paired peaks: 535 WARNING @ Tue, 14 Jul 2020 07:30:25: Fewer paired peaks (535) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 535 pairs to build model! INFO @ Tue, 14 Jul 2020 07:30:25: start model_add_line... INFO @ Tue, 14 Jul 2020 07:30:25: start X-correlation... INFO @ Tue, 14 Jul 2020 07:30:25: end of X-cor INFO @ Tue, 14 Jul 2020 07:30:25: #2 finished! INFO @ Tue, 14 Jul 2020 07:30:25: #2 predicted fragment length is 226 bps INFO @ Tue, 14 Jul 2020 07:30:25: #2 alternative fragment length(s) may be 226 bps INFO @ Tue, 14 Jul 2020 07:30:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5736468/SRX5736468.20_model.r INFO @ Tue, 14 Jul 2020 07:30:25: #3 Call peaks... INFO @ Tue, 14 Jul 2020 07:30:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 07:30:33: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 07:30:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5736468/SRX5736468.20_peaks.xls INFO @ Tue, 14 Jul 2020 07:30:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5736468/SRX5736468.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 07:30:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5736468/SRX5736468.20_summits.bed INFO @ Tue, 14 Jul 2020 07:30:37: Done! pass1 - making usageList (4 chroms): 0 millis pass2 - checking and writing primary data (300 records, 4 fields): 2 millis CompletedMACS2peakCalling