Job ID = 5721129 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 3,791,499 reads read : 7,582,998 reads written : 7,582,998 rm: cannot remove ‘[DSE]RR*’: 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 3791499 reads; of these: 3791499 (100.00%) were paired; of these: 755368 (19.92%) aligned concordantly 0 times 2299669 (60.65%) aligned concordantly exactly 1 time 736462 (19.42%) aligned concordantly >1 times ---- 755368 pairs aligned concordantly 0 times; of these: 376977 (49.91%) aligned discordantly 1 time ---- 378391 pairs aligned 0 times concordantly or discordantly; of these: 756782 mates make up the pairs; of these: 304055 (40.18%) aligned 0 times 204512 (27.02%) aligned exactly 1 time 248215 (32.80%) aligned >1 times 95.99% 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_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] 184603 / 3397273 = 0.0543 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 05:20:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708271/SRX6708271.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708271/SRX6708271.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708271/SRX6708271.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708271/SRX6708271.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 05:20:05: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:20:05: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:20:12: 1000000 INFO @ Thu, 16 Apr 2020 05:20:19: 2000000 INFO @ Thu, 16 Apr 2020 05:20:26: 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 @ Thu, 16 Apr 2020 05:20:34: 4000000 INFO @ Thu, 16 Apr 2020 05:20:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708271/SRX6708271.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708271/SRX6708271.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708271/SRX6708271.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708271/SRX6708271.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 05:20:34: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:20:34: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:20:42: 5000000 INFO @ Thu, 16 Apr 2020 05:20:42: 1000000 INFO @ Thu, 16 Apr 2020 05:20:49: 2000000 INFO @ Thu, 16 Apr 2020 05:20:50: 6000000 INFO @ Thu, 16 Apr 2020 05:20:57: 3000000 INFO @ Thu, 16 Apr 2020 05:20:57: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:20:57: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:20:57: #1 total tags in treatment: 2860808 INFO @ Thu, 16 Apr 2020 05:20:57: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:20:57: #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 05:20:57: #1 tags after filtering in treatment: 2767968 INFO @ Thu, 16 Apr 2020 05:20:57: #1 Redundant rate of treatment: 0.03 INFO @ Thu, 16 Apr 2020 05:20:57: #1 finished! INFO @ Thu, 16 Apr 2020 05:20:57: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:20:57: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:20:57: #2 number of paired peaks: 594 WARNING @ Thu, 16 Apr 2020 05:20:57: Fewer paired peaks (594) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 594 pairs to build model! INFO @ Thu, 16 Apr 2020 05:20:57: start model_add_line... INFO @ Thu, 16 Apr 2020 05:20:57: start X-correlation... INFO @ Thu, 16 Apr 2020 05:20:57: end of X-cor INFO @ Thu, 16 Apr 2020 05:20:57: #2 finished! INFO @ Thu, 16 Apr 2020 05:20:57: #2 predicted fragment length is 163 bps INFO @ Thu, 16 Apr 2020 05:20:57: #2 alternative fragment length(s) may be 163 bps INFO @ Thu, 16 Apr 2020 05:20:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708271/SRX6708271.05_model.r INFO @ Thu, 16 Apr 2020 05:20:57: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:20:57: #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 @ Thu, 16 Apr 2020 05:21:03: 4000000 INFO @ Thu, 16 Apr 2020 05:21:03: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:21:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6708271/SRX6708271.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6708271/SRX6708271.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6708271/SRX6708271.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6708271/SRX6708271.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 05:21:04: #1 read tag files... INFO @ Thu, 16 Apr 2020 05:21:04: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 05:21:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708271/SRX6708271.05_peaks.xls INFO @ Thu, 16 Apr 2020 05:21:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708271/SRX6708271.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:21:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708271/SRX6708271.05_summits.bed INFO @ Thu, 16 Apr 2020 05:21:06: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (977 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:21:10: 5000000 INFO @ Thu, 16 Apr 2020 05:21:12: 1000000 INFO @ Thu, 16 Apr 2020 05:21:17: 6000000 INFO @ Thu, 16 Apr 2020 05:21:19: 2000000 INFO @ Thu, 16 Apr 2020 05:21:24: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:21:24: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:21:24: #1 total tags in treatment: 2860808 INFO @ Thu, 16 Apr 2020 05:21:24: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:21:24: #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 05:21:24: #1 tags after filtering in treatment: 2767968 INFO @ Thu, 16 Apr 2020 05:21:24: #1 Redundant rate of treatment: 0.03 INFO @ Thu, 16 Apr 2020 05:21:24: #1 finished! INFO @ Thu, 16 Apr 2020 05:21:24: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:21:24: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:21:24: #2 number of paired peaks: 594 WARNING @ Thu, 16 Apr 2020 05:21:24: Fewer paired peaks (594) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 594 pairs to build model! INFO @ Thu, 16 Apr 2020 05:21:24: start model_add_line... INFO @ Thu, 16 Apr 2020 05:21:24: start X-correlation... INFO @ Thu, 16 Apr 2020 05:21:24: end of X-cor INFO @ Thu, 16 Apr 2020 05:21:24: #2 finished! INFO @ Thu, 16 Apr 2020 05:21:24: #2 predicted fragment length is 163 bps INFO @ Thu, 16 Apr 2020 05:21:24: #2 alternative fragment length(s) may be 163 bps INFO @ Thu, 16 Apr 2020 05:21:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708271/SRX6708271.10_model.r INFO @ Thu, 16 Apr 2020 05:21:24: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:21:24: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:21:26: 3000000 INFO @ Thu, 16 Apr 2020 05:21:30: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:21:32: 4000000 INFO @ Thu, 16 Apr 2020 05:21:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708271/SRX6708271.10_peaks.xls INFO @ Thu, 16 Apr 2020 05:21:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708271/SRX6708271.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:21:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708271/SRX6708271.10_summits.bed INFO @ Thu, 16 Apr 2020 05:21:33: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (484 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 05:21:39: 5000000 INFO @ Thu, 16 Apr 2020 05:21:45: 6000000 INFO @ Thu, 16 Apr 2020 05:21:51: #1 tag size is determined as 75 bps INFO @ Thu, 16 Apr 2020 05:21:51: #1 tag size = 75 INFO @ Thu, 16 Apr 2020 05:21:51: #1 total tags in treatment: 2860808 INFO @ Thu, 16 Apr 2020 05:21:51: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 05:21:51: #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 05:21:51: #1 tags after filtering in treatment: 2767968 INFO @ Thu, 16 Apr 2020 05:21:51: #1 Redundant rate of treatment: 0.03 INFO @ Thu, 16 Apr 2020 05:21:51: #1 finished! INFO @ Thu, 16 Apr 2020 05:21:51: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 05:21:51: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 05:21:51: #2 number of paired peaks: 594 WARNING @ Thu, 16 Apr 2020 05:21:51: Fewer paired peaks (594) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 594 pairs to build model! INFO @ Thu, 16 Apr 2020 05:21:51: start model_add_line... INFO @ Thu, 16 Apr 2020 05:21:51: start X-correlation... INFO @ Thu, 16 Apr 2020 05:21:51: end of X-cor INFO @ Thu, 16 Apr 2020 05:21:51: #2 finished! INFO @ Thu, 16 Apr 2020 05:21:51: #2 predicted fragment length is 163 bps INFO @ Thu, 16 Apr 2020 05:21:51: #2 alternative fragment length(s) may be 163 bps INFO @ Thu, 16 Apr 2020 05:21:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6708271/SRX6708271.20_model.r INFO @ Thu, 16 Apr 2020 05:21:51: #3 Call peaks... INFO @ Thu, 16 Apr 2020 05:21:51: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 05:21:57: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 05:22:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6708271/SRX6708271.20_peaks.xls INFO @ Thu, 16 Apr 2020 05:22:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6708271/SRX6708271.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 05:22:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6708271/SRX6708271.20_summits.bed INFO @ Thu, 16 Apr 2020 05:22:00: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (247 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。