Job ID = 5720605 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-15T15:42:48 fasterq-dump.2.9.6 err: cmn_iter.c cmn_read_String( #1 ).VCursorCellDataDirect() -> RC(rcNS,rcFile,rcReading,rcTransfer,rcIncomplete) spots read : 19,692,455 reads read : 19,692,455 reads written : 19,692,455 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR5289728.sra.cache’: No such file or directory 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: 00:08:03 19692455 reads; of these: 19692455 (100.00%) were unpaired; of these: 2229276 (11.32%) aligned 0 times 11133146 (56.54%) aligned exactly 1 time 6330033 (32.14%) aligned >1 times 88.68% overall alignment rate Time searching: 00:08:03 Overall time: 00:08:03 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_rmdupse_core] 6449321 / 17463179 = 0.3693 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 @ Thu, 16 Apr 2020 00:59:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592451/SRX2592451.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592451/SRX2592451.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592451/SRX2592451.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592451/SRX2592451.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 @ Thu, 16 Apr 2020 00:59:30: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:59:30: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:59:37: 1000000 INFO @ Thu, 16 Apr 2020 00:59:44: 2000000 INFO @ Thu, 16 Apr 2020 00:59:51: 3000000 INFO @ Thu, 16 Apr 2020 00:59:58: 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 @ Thu, 16 Apr 2020 01:00:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592451/SRX2592451.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592451/SRX2592451.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592451/SRX2592451.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592451/SRX2592451.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 @ Thu, 16 Apr 2020 01:00:00: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:00:00: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:00:05: 5000000 INFO @ Thu, 16 Apr 2020 01:00:07: 1000000 INFO @ Thu, 16 Apr 2020 01:00:12: 6000000 INFO @ Thu, 16 Apr 2020 01:00:14: 2000000 INFO @ Thu, 16 Apr 2020 01:00:20: 7000000 INFO @ Thu, 16 Apr 2020 01:00:22: 3000000 INFO @ Thu, 16 Apr 2020 01:00:27: 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 @ Thu, 16 Apr 2020 01:00:29: 4000000 INFO @ Thu, 16 Apr 2020 01:00:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592451/SRX2592451.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592451/SRX2592451.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592451/SRX2592451.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592451/SRX2592451.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 @ Thu, 16 Apr 2020 01:00:30: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:00:30: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:00:34: 9000000 INFO @ Thu, 16 Apr 2020 01:00:37: 5000000 INFO @ Thu, 16 Apr 2020 01:00:37: 1000000 INFO @ Thu, 16 Apr 2020 01:00:42: 10000000 INFO @ Thu, 16 Apr 2020 01:00:44: 6000000 INFO @ Thu, 16 Apr 2020 01:00:46: 2000000 INFO @ Thu, 16 Apr 2020 01:00:49: 11000000 INFO @ Thu, 16 Apr 2020 01:00:49: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 01:00:49: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 01:00:49: #1 total tags in treatment: 11013858 INFO @ Thu, 16 Apr 2020 01:00:49: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:00:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 01:00:49: #1 tags after filtering in treatment: 11013858 INFO @ Thu, 16 Apr 2020 01:00:49: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:00:49: #1 finished! INFO @ Thu, 16 Apr 2020 01:00:49: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:00:49: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:00:50: #2 number of paired peaks: 228 WARNING @ Thu, 16 Apr 2020 01:00:50: Fewer paired peaks (228) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 228 pairs to build model! INFO @ Thu, 16 Apr 2020 01:00:50: start model_add_line... INFO @ Thu, 16 Apr 2020 01:00:50: start X-correlation... INFO @ Thu, 16 Apr 2020 01:00:50: end of X-cor INFO @ Thu, 16 Apr 2020 01:00:50: #2 finished! INFO @ Thu, 16 Apr 2020 01:00:50: #2 predicted fragment length is 293 bps INFO @ Thu, 16 Apr 2020 01:00:50: #2 alternative fragment length(s) may be 293 bps INFO @ Thu, 16 Apr 2020 01:00:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592451/SRX2592451.05_model.r INFO @ Thu, 16 Apr 2020 01:00:50: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:00:50: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:00:52: 7000000 INFO @ Thu, 16 Apr 2020 01:00:54: 3000000 INFO @ Thu, 16 Apr 2020 01:00:59: 8000000 INFO @ Thu, 16 Apr 2020 01:01:01: 4000000 INFO @ Thu, 16 Apr 2020 01:01:07: 9000000 INFO @ Thu, 16 Apr 2020 01:01:09: 5000000 INFO @ Thu, 16 Apr 2020 01:01:14: 10000000 INFO @ Thu, 16 Apr 2020 01:01:16: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:01:17: 6000000 INFO @ Thu, 16 Apr 2020 01:01:21: 11000000 INFO @ Thu, 16 Apr 2020 01:01:21: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 01:01:21: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 01:01:21: #1 total tags in treatment: 11013858 INFO @ Thu, 16 Apr 2020 01:01:21: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:01:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 01:01:21: #1 tags after filtering in treatment: 11013858 INFO @ Thu, 16 Apr 2020 01:01:21: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:01:21: #1 finished! INFO @ Thu, 16 Apr 2020 01:01:21: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:01:21: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:01:22: #2 number of paired peaks: 228 WARNING @ Thu, 16 Apr 2020 01:01:22: Fewer paired peaks (228) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 228 pairs to build model! INFO @ Thu, 16 Apr 2020 01:01:22: start model_add_line... INFO @ Thu, 16 Apr 2020 01:01:22: start X-correlation... INFO @ Thu, 16 Apr 2020 01:01:22: end of X-cor INFO @ Thu, 16 Apr 2020 01:01:22: #2 finished! INFO @ Thu, 16 Apr 2020 01:01:22: #2 predicted fragment length is 293 bps INFO @ Thu, 16 Apr 2020 01:01:22: #2 alternative fragment length(s) may be 293 bps INFO @ Thu, 16 Apr 2020 01:01:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592451/SRX2592451.10_model.r INFO @ Thu, 16 Apr 2020 01:01:22: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:01:22: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:01:24: 7000000 INFO @ Thu, 16 Apr 2020 01:01:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592451/SRX2592451.05_peaks.xls INFO @ Thu, 16 Apr 2020 01:01:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592451/SRX2592451.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:01:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592451/SRX2592451.05_summits.bed INFO @ Thu, 16 Apr 2020 01:01:30: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (15557 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:01:32: 8000000 INFO @ Thu, 16 Apr 2020 01:01:39: 9000000 INFO @ Thu, 16 Apr 2020 01:01:46: 10000000 INFO @ Thu, 16 Apr 2020 01:01:49: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:01:53: 11000000 INFO @ Thu, 16 Apr 2020 01:01:53: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 01:01:53: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 01:01:53: #1 total tags in treatment: 11013858 INFO @ Thu, 16 Apr 2020 01:01:53: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:01:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 01:01:53: #1 tags after filtering in treatment: 11013858 INFO @ Thu, 16 Apr 2020 01:01:53: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:01:53: #1 finished! INFO @ Thu, 16 Apr 2020 01:01:53: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:01:53: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:01:55: #2 number of paired peaks: 228 WARNING @ Thu, 16 Apr 2020 01:01:55: Fewer paired peaks (228) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 228 pairs to build model! INFO @ Thu, 16 Apr 2020 01:01:55: start model_add_line... INFO @ Thu, 16 Apr 2020 01:01:55: start X-correlation... INFO @ Thu, 16 Apr 2020 01:01:55: end of X-cor INFO @ Thu, 16 Apr 2020 01:01:55: #2 finished! INFO @ Thu, 16 Apr 2020 01:01:55: #2 predicted fragment length is 293 bps INFO @ Thu, 16 Apr 2020 01:01:55: #2 alternative fragment length(s) may be 293 bps INFO @ Thu, 16 Apr 2020 01:01:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592451/SRX2592451.20_model.r INFO @ Thu, 16 Apr 2020 01:01:55: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:01:55: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:02:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592451/SRX2592451.10_peaks.xls INFO @ Thu, 16 Apr 2020 01:02:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592451/SRX2592451.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:02:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592451/SRX2592451.10_summits.bed INFO @ Thu, 16 Apr 2020 01:02:03: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (11740 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:02:22: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 16 Apr 2020 01:02:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592451/SRX2592451.20_peaks.xls INFO @ Thu, 16 Apr 2020 01:02:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592451/SRX2592451.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:02:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592451/SRX2592451.20_summits.bed INFO @ Thu, 16 Apr 2020 01:02:35: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (7775 records, 4 fields): 8 millis CompletedMACS2peakCalling BigWig に変換しました。