Job ID = 6498691 SRX = SRX699117 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-25T23:59:49 prefetch.2.10.7: 1) Downloading 'SRR1573165'... 2020-06-25T23:59:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T00:01:08 prefetch.2.10.7: HTTPS download succeed 2020-06-26T00:01:08 prefetch.2.10.7: 'SRR1573165' is valid 2020-06-26T00:01:08 prefetch.2.10.7: 1) 'SRR1573165' was downloaded successfully Read 3100142 spots for SRR1573165/SRR1573165.sra Written 3100142 spots for SRR1573165/SRR1573165.sra 2020-06-26T00:01:42 prefetch.2.10.7: 1) Downloading 'SRR1573166'... 2020-06-26T00:01:42 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T00:02:47 prefetch.2.10.7: HTTPS download succeed 2020-06-26T00:02:48 prefetch.2.10.7: 'SRR1573166' is valid 2020-06-26T00:02:48 prefetch.2.10.7: 1) 'SRR1573166' was downloaded successfully Read 3144273 spots for SRR1573166/SRR1573166.sra Written 3144273 spots for SRR1573166/SRR1573166.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: 00:10:18 6244415 reads; of these: 6244415 (100.00%) were paired; of these: 207113 (3.32%) aligned concordantly 0 times 5363858 (85.90%) aligned concordantly exactly 1 time 673444 (10.78%) aligned concordantly >1 times ---- 207113 pairs aligned concordantly 0 times; of these: 17970 (8.68%) aligned discordantly 1 time ---- 189143 pairs aligned 0 times concordantly or discordantly; of these: 378286 mates make up the pairs; of these: 223903 (59.19%) aligned 0 times 110725 (29.27%) aligned exactly 1 time 43658 (11.54%) aligned >1 times 98.21% overall alignment rate Time searching: 00:10:18 Overall time: 00:10:18 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] 349329 / 6051440 = 0.0577 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 09:19:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX699117/SRX699117.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX699117/SRX699117.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX699117/SRX699117.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX699117/SRX699117.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 09:19:06: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:19:06: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:19:12: 1000000 INFO @ Fri, 26 Jun 2020 09:19:19: 2000000 INFO @ Fri, 26 Jun 2020 09:19:25: 3000000 INFO @ Fri, 26 Jun 2020 09:19:32: 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 09:19:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX699117/SRX699117.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX699117/SRX699117.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX699117/SRX699117.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX699117/SRX699117.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 09:19:36: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:19:36: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:19:38: 5000000 INFO @ Fri, 26 Jun 2020 09:19:43: 1000000 INFO @ Fri, 26 Jun 2020 09:19:46: 6000000 INFO @ Fri, 26 Jun 2020 09:19:51: 2000000 INFO @ Fri, 26 Jun 2020 09:19:53: 7000000 INFO @ Fri, 26 Jun 2020 09:19:58: 3000000 INFO @ Fri, 26 Jun 2020 09:20:00: 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 09:20:05: 4000000 INFO @ Fri, 26 Jun 2020 09:20:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX699117/SRX699117.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX699117/SRX699117.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX699117/SRX699117.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX699117/SRX699117.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 09:20:06: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:20:06: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:20:07: 9000000 INFO @ Fri, 26 Jun 2020 09:20:12: 5000000 INFO @ Fri, 26 Jun 2020 09:20:13: 1000000 INFO @ Fri, 26 Jun 2020 09:20:15: 10000000 INFO @ Fri, 26 Jun 2020 09:20:20: 6000000 INFO @ Fri, 26 Jun 2020 09:20:21: 2000000 INFO @ Fri, 26 Jun 2020 09:20:22: 11000000 INFO @ Fri, 26 Jun 2020 09:20:26: #1 tag size is determined as 101 bps INFO @ Fri, 26 Jun 2020 09:20:26: #1 tag size = 101 INFO @ Fri, 26 Jun 2020 09:20:26: #1 total tags in treatment: 5688837 INFO @ Fri, 26 Jun 2020 09:20:26: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:20:26: #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 09:20:26: #1 tags after filtering in treatment: 5458247 INFO @ Fri, 26 Jun 2020 09:20:26: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 26 Jun 2020 09:20:26: #1 finished! INFO @ Fri, 26 Jun 2020 09:20:26: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:20:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:20:27: #2 number of paired peaks: 802 WARNING @ Fri, 26 Jun 2020 09:20:27: Fewer paired peaks (802) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 802 pairs to build model! INFO @ Fri, 26 Jun 2020 09:20:27: start model_add_line... INFO @ Fri, 26 Jun 2020 09:20:27: start X-correlation... INFO @ Fri, 26 Jun 2020 09:20:27: end of X-cor INFO @ Fri, 26 Jun 2020 09:20:27: #2 finished! INFO @ Fri, 26 Jun 2020 09:20:27: #2 predicted fragment length is 206 bps INFO @ Fri, 26 Jun 2020 09:20:27: #2 alternative fragment length(s) may be 206 bps INFO @ Fri, 26 Jun 2020 09:20:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX699117/SRX699117.05_model.r INFO @ Fri, 26 Jun 2020 09:20:27: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:20:27: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:20:27: 7000000 INFO @ Fri, 26 Jun 2020 09:20:28: 3000000 INFO @ Fri, 26 Jun 2020 09:20:34: 8000000 INFO @ Fri, 26 Jun 2020 09:20:35: 4000000 INFO @ Fri, 26 Jun 2020 09:20:39: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:20:42: 9000000 INFO @ Fri, 26 Jun 2020 09:20:43: 5000000 INFO @ Fri, 26 Jun 2020 09:20:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX699117/SRX699117.05_peaks.xls INFO @ Fri, 26 Jun 2020 09:20:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX699117/SRX699117.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:20:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX699117/SRX699117.05_summits.bed INFO @ Fri, 26 Jun 2020 09:20:46: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1994 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:20:49: 10000000 INFO @ Fri, 26 Jun 2020 09:20:50: 6000000 INFO @ Fri, 26 Jun 2020 09:20:56: 11000000 INFO @ Fri, 26 Jun 2020 09:20:57: 7000000 INFO @ Fri, 26 Jun 2020 09:21:00: #1 tag size is determined as 101 bps INFO @ Fri, 26 Jun 2020 09:21:00: #1 tag size = 101 INFO @ Fri, 26 Jun 2020 09:21:00: #1 total tags in treatment: 5688837 INFO @ Fri, 26 Jun 2020 09:21:00: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:21:00: #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 09:21:01: #1 tags after filtering in treatment: 5458247 INFO @ Fri, 26 Jun 2020 09:21:01: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 26 Jun 2020 09:21:01: #1 finished! INFO @ Fri, 26 Jun 2020 09:21:01: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:21:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:21:01: #2 number of paired peaks: 802 WARNING @ Fri, 26 Jun 2020 09:21:01: Fewer paired peaks (802) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 802 pairs to build model! INFO @ Fri, 26 Jun 2020 09:21:01: start model_add_line... INFO @ Fri, 26 Jun 2020 09:21:01: start X-correlation... INFO @ Fri, 26 Jun 2020 09:21:01: end of X-cor INFO @ Fri, 26 Jun 2020 09:21:01: #2 finished! INFO @ Fri, 26 Jun 2020 09:21:01: #2 predicted fragment length is 206 bps INFO @ Fri, 26 Jun 2020 09:21:01: #2 alternative fragment length(s) may be 206 bps INFO @ Fri, 26 Jun 2020 09:21:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX699117/SRX699117.10_model.r INFO @ Fri, 26 Jun 2020 09:21:01: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:21:01: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:21:04: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 09:21:11: 9000000 INFO @ Fri, 26 Jun 2020 09:21:13: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:21:18: 10000000 INFO @ Fri, 26 Jun 2020 09:21:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX699117/SRX699117.10_peaks.xls INFO @ Fri, 26 Jun 2020 09:21:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX699117/SRX699117.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:21:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX699117/SRX699117.10_summits.bed INFO @ Fri, 26 Jun 2020 09:21:20: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (450 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:21:25: 11000000 BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 09:21:29: #1 tag size is determined as 101 bps INFO @ Fri, 26 Jun 2020 09:21:29: #1 tag size = 101 INFO @ Fri, 26 Jun 2020 09:21:29: #1 total tags in treatment: 5688837 INFO @ Fri, 26 Jun 2020 09:21:29: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:21:29: #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 09:21:29: #1 tags after filtering in treatment: 5458247 INFO @ Fri, 26 Jun 2020 09:21:29: #1 Redundant rate of treatment: 0.04 INFO @ Fri, 26 Jun 2020 09:21:29: #1 finished! INFO @ Fri, 26 Jun 2020 09:21:29: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:21:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:21:29: #2 number of paired peaks: 802 WARNING @ Fri, 26 Jun 2020 09:21:29: Fewer paired peaks (802) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 802 pairs to build model! INFO @ Fri, 26 Jun 2020 09:21:29: start model_add_line... INFO @ Fri, 26 Jun 2020 09:21:29: start X-correlation... INFO @ Fri, 26 Jun 2020 09:21:30: end of X-cor INFO @ Fri, 26 Jun 2020 09:21:30: #2 finished! INFO @ Fri, 26 Jun 2020 09:21:30: #2 predicted fragment length is 206 bps INFO @ Fri, 26 Jun 2020 09:21:30: #2 alternative fragment length(s) may be 206 bps INFO @ Fri, 26 Jun 2020 09:21:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX699117/SRX699117.20_model.r INFO @ Fri, 26 Jun 2020 09:21:30: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:21:30: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:21:43: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:21:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX699117/SRX699117.20_peaks.xls INFO @ Fri, 26 Jun 2020 09:21:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX699117/SRX699117.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:21:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX699117/SRX699117.20_summits.bed INFO @ Fri, 26 Jun 2020 09:21:49: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (165 records, 4 fields): 3 millis CompletedMACS2peakCalling