Job ID = 5721269 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 19,882,025 reads read : 39,764,050 reads written : 19,882,025 reads 0-length : 19,882,025 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: 00:05:17 19882025 reads; of these: 19882025 (100.00%) were unpaired; of these: 4050101 (20.37%) aligned 0 times 11418526 (57.43%) aligned exactly 1 time 4413398 (22.20%) aligned >1 times 79.63% overall alignment rate Time searching: 00:05:17 Overall time: 00:05:17 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] 10267595 / 15831924 = 0.6485 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 06:23:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7277044/SRX7277044.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7277044/SRX7277044.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7277044/SRX7277044.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7277044/SRX7277044.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 06:23:24: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:23:24: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:23:31: 1000000 INFO @ Thu, 16 Apr 2020 06:23:39: 2000000 INFO @ Thu, 16 Apr 2020 06:23:46: 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 06:23:54: 4000000 INFO @ Thu, 16 Apr 2020 06:23:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7277044/SRX7277044.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7277044/SRX7277044.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7277044/SRX7277044.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7277044/SRX7277044.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 06:23:54: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:23:54: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:24:00: 1000000 INFO @ Thu, 16 Apr 2020 06:24:01: 5000000 INFO @ Thu, 16 Apr 2020 06:24:05: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 06:24:05: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 06:24:05: #1 total tags in treatment: 5564329 INFO @ Thu, 16 Apr 2020 06:24:05: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:24:05: #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 06:24:05: #1 tags after filtering in treatment: 5564329 INFO @ Thu, 16 Apr 2020 06:24:05: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 06:24:05: #1 finished! INFO @ Thu, 16 Apr 2020 06:24:05: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:24:05: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:24:06: #2 number of paired peaks: 510 WARNING @ Thu, 16 Apr 2020 06:24:06: Fewer paired peaks (510) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 510 pairs to build model! INFO @ Thu, 16 Apr 2020 06:24:06: start model_add_line... INFO @ Thu, 16 Apr 2020 06:24:06: start X-correlation... INFO @ Thu, 16 Apr 2020 06:24:06: end of X-cor INFO @ Thu, 16 Apr 2020 06:24:06: #2 finished! INFO @ Thu, 16 Apr 2020 06:24:06: #2 predicted fragment length is 75 bps INFO @ Thu, 16 Apr 2020 06:24:06: #2 alternative fragment length(s) may be 75 bps INFO @ Thu, 16 Apr 2020 06:24:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7277044/SRX7277044.05_model.r WARNING @ Thu, 16 Apr 2020 06:24:06: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:24:06: #2 You may need to consider one of the other alternative d(s): 75 WARNING @ Thu, 16 Apr 2020 06:24:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 06:24:06: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:24:06: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:24:06: 2000000 INFO @ Thu, 16 Apr 2020 06:24:12: 3000000 INFO @ Thu, 16 Apr 2020 06:24:18: 4000000 INFO @ Thu, 16 Apr 2020 06:24:19: #3 Call peaks for each chromosome... 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 06:24:24: 5000000 INFO @ Thu, 16 Apr 2020 06:24:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7277044/SRX7277044.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7277044/SRX7277044.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7277044/SRX7277044.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7277044/SRX7277044.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 06:24:24: #1 read tag files... INFO @ Thu, 16 Apr 2020 06:24:24: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 06:24:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7277044/SRX7277044.05_peaks.xls INFO @ Thu, 16 Apr 2020 06:24:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7277044/SRX7277044.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:24:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7277044/SRX7277044.05_summits.bed INFO @ Thu, 16 Apr 2020 06:24:25: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2005 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:24:27: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 06:24:27: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 06:24:27: #1 total tags in treatment: 5564329 INFO @ Thu, 16 Apr 2020 06:24:27: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:24:27: #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 06:24:27: #1 tags after filtering in treatment: 5564329 INFO @ Thu, 16 Apr 2020 06:24:27: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 06:24:27: #1 finished! INFO @ Thu, 16 Apr 2020 06:24:27: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:24:27: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:24:28: #2 number of paired peaks: 510 WARNING @ Thu, 16 Apr 2020 06:24:28: Fewer paired peaks (510) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 510 pairs to build model! INFO @ Thu, 16 Apr 2020 06:24:28: start model_add_line... INFO @ Thu, 16 Apr 2020 06:24:28: start X-correlation... INFO @ Thu, 16 Apr 2020 06:24:28: end of X-cor INFO @ Thu, 16 Apr 2020 06:24:28: #2 finished! INFO @ Thu, 16 Apr 2020 06:24:28: #2 predicted fragment length is 75 bps INFO @ Thu, 16 Apr 2020 06:24:28: #2 alternative fragment length(s) may be 75 bps INFO @ Thu, 16 Apr 2020 06:24:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7277044/SRX7277044.10_model.r WARNING @ Thu, 16 Apr 2020 06:24:28: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:24:28: #2 You may need to consider one of the other alternative d(s): 75 WARNING @ Thu, 16 Apr 2020 06:24:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 06:24:28: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:24:28: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:24:30: 1000000 INFO @ Thu, 16 Apr 2020 06:24:36: 2000000 INFO @ Thu, 16 Apr 2020 06:24:39: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:24:42: 3000000 INFO @ Thu, 16 Apr 2020 06:24:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7277044/SRX7277044.10_peaks.xls INFO @ Thu, 16 Apr 2020 06:24:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7277044/SRX7277044.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:24:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7277044/SRX7277044.10_summits.bed INFO @ Thu, 16 Apr 2020 06:24:46: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1186 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 06:24:47: 4000000 INFO @ Thu, 16 Apr 2020 06:24:53: 5000000 INFO @ Thu, 16 Apr 2020 06:24:56: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 06:24:56: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 06:24:56: #1 total tags in treatment: 5564329 INFO @ Thu, 16 Apr 2020 06:24:56: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 06:24:56: #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 06:24:56: #1 tags after filtering in treatment: 5564329 INFO @ Thu, 16 Apr 2020 06:24:56: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 06:24:56: #1 finished! INFO @ Thu, 16 Apr 2020 06:24:56: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 06:24:56: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 06:24:57: #2 number of paired peaks: 510 WARNING @ Thu, 16 Apr 2020 06:24:57: Fewer paired peaks (510) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 510 pairs to build model! INFO @ Thu, 16 Apr 2020 06:24:57: start model_add_line... INFO @ Thu, 16 Apr 2020 06:24:57: start X-correlation... INFO @ Thu, 16 Apr 2020 06:24:57: end of X-cor INFO @ Thu, 16 Apr 2020 06:24:57: #2 finished! INFO @ Thu, 16 Apr 2020 06:24:57: #2 predicted fragment length is 75 bps INFO @ Thu, 16 Apr 2020 06:24:57: #2 alternative fragment length(s) may be 75 bps INFO @ Thu, 16 Apr 2020 06:24:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7277044/SRX7277044.20_model.r WARNING @ Thu, 16 Apr 2020 06:24:57: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 06:24:57: #2 You may need to consider one of the other alternative d(s): 75 WARNING @ Thu, 16 Apr 2020 06:24:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 06:24:57: #3 Call peaks... INFO @ Thu, 16 Apr 2020 06:24:57: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 06:25:09: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 06:25:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7277044/SRX7277044.20_peaks.xls INFO @ Thu, 16 Apr 2020 06:25:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7277044/SRX7277044.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 06:25:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7277044/SRX7277044.20_summits.bed INFO @ Thu, 16 Apr 2020 06:25:15: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (586 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。