Job ID = 6459295 SRX = SRX661232 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:05:01 prefetch.2.10.7: 1) Downloading 'SRR1524960'... 2020-06-21T13:05:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:06:01 prefetch.2.10.7 int: timeout exhausted while creating file within network system module - Cannot KNSManagerMakeClientRequest: https://sra-downloadb.be-md.ncbi.nlm.nih.gov/sos1/sra-pub-run-5/SRR1524960/SRR1524960.1 2020-06-21T13:06:01 prefetch.2.10.7: HTTPS download failed 2020-06-21T13:06:01 prefetch.2.10.7: 1) failed to download SRR1524960 2020-06-21T13:06:11 prefetch.2.10.7: 1) Downloading 'SRR1524960'... 2020-06-21T13:06:11 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:08:11 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:08:11 prefetch.2.10.7: 1) 'SRR1524960' was downloaded successfully Read 19135694 spots for SRR1524960/SRR1524960.sra Written 19135694 spots for SRR1524960/SRR1524960.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: 00:02:54 19135694 reads; of these: 19135694 (100.00%) were unpaired; of these: 12108794 (63.28%) aligned 0 times 6019163 (31.46%) aligned exactly 1 time 1007737 (5.27%) aligned >1 times 36.72% overall alignment rate Time searching: 00:02:54 Overall time: 00:02:54 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_rmdupse_core] 5890856 / 7026900 = 0.8383 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 @ Sun, 21 Jun 2020 22:13:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX661232/SRX661232.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX661232/SRX661232.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX661232/SRX661232.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX661232/SRX661232.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 @ Sun, 21 Jun 2020 22:13:37: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:13:37: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:13:43: 1000000 INFO @ Sun, 21 Jun 2020 22:13:44: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:13:44: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:13:44: #1 total tags in treatment: 1136044 INFO @ Sun, 21 Jun 2020 22:13:44: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:13:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 22:13:44: #1 tags after filtering in treatment: 1135783 INFO @ Sun, 21 Jun 2020 22:13:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:13:44: #1 finished! INFO @ Sun, 21 Jun 2020 22:13:44: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:13:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:13:44: #2 number of paired peaks: 2396 INFO @ Sun, 21 Jun 2020 22:13:44: start model_add_line... INFO @ Sun, 21 Jun 2020 22:13:44: start X-correlation... INFO @ Sun, 21 Jun 2020 22:13:45: end of X-cor INFO @ Sun, 21 Jun 2020 22:13:45: #2 finished! INFO @ Sun, 21 Jun 2020 22:13:45: #2 predicted fragment length is 114 bps INFO @ Sun, 21 Jun 2020 22:13:45: #2 alternative fragment length(s) may be 114 bps INFO @ Sun, 21 Jun 2020 22:13:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX661232/SRX661232.05_model.r INFO @ Sun, 21 Jun 2020 22:13:45: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:13:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:13:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:13:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX661232/SRX661232.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:13:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX661232/SRX661232.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:13:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX661232/SRX661232.05_summits.bed INFO @ Sun, 21 Jun 2020 22:13:49: Done! pass1 - making usageList (138 chroms): 1 millis pass2 - checking and writing primary data (369 records, 4 fields): 5 millis CompletedMACS2peakCalling 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 @ Sun, 21 Jun 2020 22:14:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX661232/SRX661232.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX661232/SRX661232.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX661232/SRX661232.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX661232/SRX661232.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 @ Sun, 21 Jun 2020 22:14:07: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:14:07: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:14:13: 1000000 INFO @ Sun, 21 Jun 2020 22:14:14: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:14:14: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:14:14: #1 total tags in treatment: 1136044 INFO @ Sun, 21 Jun 2020 22:14:14: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:14:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 22:14:14: #1 tags after filtering in treatment: 1135783 INFO @ Sun, 21 Jun 2020 22:14:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:14:14: #1 finished! INFO @ Sun, 21 Jun 2020 22:14:14: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:14:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:14:14: #2 number of paired peaks: 2396 INFO @ Sun, 21 Jun 2020 22:14:14: start model_add_line... INFO @ Sun, 21 Jun 2020 22:14:14: start X-correlation... INFO @ Sun, 21 Jun 2020 22:14:14: end of X-cor INFO @ Sun, 21 Jun 2020 22:14:14: #2 finished! INFO @ Sun, 21 Jun 2020 22:14:14: #2 predicted fragment length is 114 bps INFO @ Sun, 21 Jun 2020 22:14:14: #2 alternative fragment length(s) may be 114 bps INFO @ Sun, 21 Jun 2020 22:14:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX661232/SRX661232.10_model.r INFO @ Sun, 21 Jun 2020 22:14:14: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:14:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:14:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:14:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX661232/SRX661232.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:14:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX661232/SRX661232.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:14:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX661232/SRX661232.10_summits.bed INFO @ Sun, 21 Jun 2020 22:14:19: Done! pass1 - making usageList (90 chroms): 1 millis pass2 - checking and writing primary data (195 records, 4 fields): 4 millis CompletedMACS2peakCalling 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 @ Sun, 21 Jun 2020 22:14:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX661232/SRX661232.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX661232/SRX661232.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX661232/SRX661232.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX661232/SRX661232.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 @ Sun, 21 Jun 2020 22:14:37: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:14:37: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:14:43: 1000000 INFO @ Sun, 21 Jun 2020 22:14:44: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 22:14:44: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 22:14:44: #1 total tags in treatment: 1136044 INFO @ Sun, 21 Jun 2020 22:14:44: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:14:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 22:14:44: #1 tags after filtering in treatment: 1135783 INFO @ Sun, 21 Jun 2020 22:14:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:14:44: #1 finished! INFO @ Sun, 21 Jun 2020 22:14:44: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:14:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:14:44: #2 number of paired peaks: 2396 INFO @ Sun, 21 Jun 2020 22:14:44: start model_add_line... INFO @ Sun, 21 Jun 2020 22:14:44: start X-correlation... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:14:44: end of X-cor INFO @ Sun, 21 Jun 2020 22:14:44: #2 finished! INFO @ Sun, 21 Jun 2020 22:14:44: #2 predicted fragment length is 114 bps INFO @ Sun, 21 Jun 2020 22:14:44: #2 alternative fragment length(s) may be 114 bps INFO @ Sun, 21 Jun 2020 22:14:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX661232/SRX661232.20_model.r INFO @ Sun, 21 Jun 2020 22:14:44: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:14:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:14:48: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:14:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX661232/SRX661232.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:14:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX661232/SRX661232.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:14:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX661232/SRX661232.20_summits.bed INFO @ Sun, 21 Jun 2020 22:14:49: Done! pass1 - making usageList (72 chroms): 1 millis pass2 - checking and writing primary data (116 records, 4 fields): 3 millis CompletedMACS2peakCalling