Job ID = 6529531 SRX = SRX287973 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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: 00:00:01 Multiseed full-index search: 00:05:37 17599879 reads; of these: 17599879 (100.00%) were unpaired; of these: 993100 (5.64%) aligned 0 times 11531413 (65.52%) aligned exactly 1 time 5075366 (28.84%) aligned >1 times 94.36% overall alignment rate Time searching: 00:05:38 Overall time: 00:05:38 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_sort_core] merging from 8 files... [bam_rmdupse_core] 1583959 / 16606779 = 0.0954 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 @ Tue, 30 Jun 2020 02:14:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287973/SRX287973.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287973/SRX287973.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287973/SRX287973.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287973/SRX287973.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 @ Tue, 30 Jun 2020 02:14:38: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:14:38: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:14:44: 1000000 INFO @ Tue, 30 Jun 2020 02:14:51: 2000000 INFO @ Tue, 30 Jun 2020 02:14:58: 3000000 INFO @ Tue, 30 Jun 2020 02:15:04: 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 @ Tue, 30 Jun 2020 02:15:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287973/SRX287973.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287973/SRX287973.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287973/SRX287973.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287973/SRX287973.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 @ Tue, 30 Jun 2020 02:15:08: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:15:08: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:15:11: 5000000 INFO @ Tue, 30 Jun 2020 02:15:15: 1000000 INFO @ Tue, 30 Jun 2020 02:15:17: 6000000 INFO @ Tue, 30 Jun 2020 02:15:23: 2000000 INFO @ Tue, 30 Jun 2020 02:15:24: 7000000 INFO @ Tue, 30 Jun 2020 02:15:30: 3000000 INFO @ Tue, 30 Jun 2020 02:15:31: 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 @ Tue, 30 Jun 2020 02:15:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287973/SRX287973.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287973/SRX287973.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287973/SRX287973.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287973/SRX287973.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 @ Tue, 30 Jun 2020 02:15:38: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:15:38: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:15:38: 9000000 INFO @ Tue, 30 Jun 2020 02:15:38: 4000000 INFO @ Tue, 30 Jun 2020 02:15:45: 10000000 INFO @ Tue, 30 Jun 2020 02:15:45: 1000000 INFO @ Tue, 30 Jun 2020 02:15:46: 5000000 INFO @ Tue, 30 Jun 2020 02:15:52: 11000000 INFO @ Tue, 30 Jun 2020 02:15:53: 2000000 INFO @ Tue, 30 Jun 2020 02:15:53: 6000000 INFO @ Tue, 30 Jun 2020 02:16:00: 3000000 INFO @ Tue, 30 Jun 2020 02:16:00: 12000000 INFO @ Tue, 30 Jun 2020 02:16:01: 7000000 INFO @ Tue, 30 Jun 2020 02:16:07: 4000000 INFO @ Tue, 30 Jun 2020 02:16:08: 13000000 INFO @ Tue, 30 Jun 2020 02:16:08: 8000000 INFO @ Tue, 30 Jun 2020 02:16:15: 5000000 INFO @ Tue, 30 Jun 2020 02:16:16: 14000000 INFO @ Tue, 30 Jun 2020 02:16:16: 9000000 INFO @ Tue, 30 Jun 2020 02:16:22: 6000000 INFO @ Tue, 30 Jun 2020 02:16:23: 10000000 INFO @ Tue, 30 Jun 2020 02:16:24: 15000000 INFO @ Tue, 30 Jun 2020 02:16:24: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:16:24: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:16:24: #1 total tags in treatment: 15022820 INFO @ Tue, 30 Jun 2020 02:16:24: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:16:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:16:25: #1 tags after filtering in treatment: 15022818 INFO @ Tue, 30 Jun 2020 02:16:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:16:25: #1 finished! INFO @ Tue, 30 Jun 2020 02:16:25: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:16:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:16:26: #2 number of paired peaks: 696 WARNING @ Tue, 30 Jun 2020 02:16:26: Fewer paired peaks (696) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 696 pairs to build model! INFO @ Tue, 30 Jun 2020 02:16:26: start model_add_line... INFO @ Tue, 30 Jun 2020 02:16:26: start X-correlation... INFO @ Tue, 30 Jun 2020 02:16:26: end of X-cor INFO @ Tue, 30 Jun 2020 02:16:26: #2 finished! INFO @ Tue, 30 Jun 2020 02:16:26: #2 predicted fragment length is 39 bps INFO @ Tue, 30 Jun 2020 02:16:26: #2 alternative fragment length(s) may be 3,39 bps INFO @ Tue, 30 Jun 2020 02:16:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287973/SRX287973.05_model.r WARNING @ Tue, 30 Jun 2020 02:16:26: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:16:26: #2 You may need to consider one of the other alternative d(s): 3,39 WARNING @ Tue, 30 Jun 2020 02:16:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:16:26: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:16:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:16:29: 7000000 INFO @ Tue, 30 Jun 2020 02:16:31: 11000000 INFO @ Tue, 30 Jun 2020 02:16:36: 8000000 INFO @ Tue, 30 Jun 2020 02:16:38: 12000000 INFO @ Tue, 30 Jun 2020 02:16:43: 9000000 INFO @ Tue, 30 Jun 2020 02:16:46: 13000000 INFO @ Tue, 30 Jun 2020 02:16:49: 10000000 INFO @ Tue, 30 Jun 2020 02:16:52: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:16:54: 14000000 INFO @ Tue, 30 Jun 2020 02:16:56: 11000000 INFO @ Tue, 30 Jun 2020 02:17:01: 15000000 INFO @ Tue, 30 Jun 2020 02:17:02: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:17:02: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:17:02: #1 total tags in treatment: 15022820 INFO @ Tue, 30 Jun 2020 02:17:02: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:17:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:17:03: #1 tags after filtering in treatment: 15022818 INFO @ Tue, 30 Jun 2020 02:17:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:17:03: #1 finished! INFO @ Tue, 30 Jun 2020 02:17:03: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:17:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:17:03: 12000000 INFO @ Tue, 30 Jun 2020 02:17:04: #2 number of paired peaks: 696 WARNING @ Tue, 30 Jun 2020 02:17:04: Fewer paired peaks (696) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 696 pairs to build model! INFO @ Tue, 30 Jun 2020 02:17:04: start model_add_line... INFO @ Tue, 30 Jun 2020 02:17:04: start X-correlation... INFO @ Tue, 30 Jun 2020 02:17:04: end of X-cor INFO @ Tue, 30 Jun 2020 02:17:04: #2 finished! INFO @ Tue, 30 Jun 2020 02:17:04: #2 predicted fragment length is 39 bps INFO @ Tue, 30 Jun 2020 02:17:04: #2 alternative fragment length(s) may be 3,39 bps INFO @ Tue, 30 Jun 2020 02:17:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287973/SRX287973.10_model.r WARNING @ Tue, 30 Jun 2020 02:17:04: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:17:04: #2 You may need to consider one of the other alternative d(s): 3,39 WARNING @ Tue, 30 Jun 2020 02:17:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:17:04: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:17:04: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:17:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287973/SRX287973.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:17:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287973/SRX287973.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:17:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287973/SRX287973.05_summits.bed INFO @ Tue, 30 Jun 2020 02:17:07: Done! pass1 - making usageList (684 chroms): 1 millis pass2 - checking and writing primary data (2716 records, 4 fields): 43 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:17:10: 13000000 INFO @ Tue, 30 Jun 2020 02:17:17: 14000000 INFO @ Tue, 30 Jun 2020 02:17:25: 15000000 INFO @ Tue, 30 Jun 2020 02:17:25: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:17:25: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:17:25: #1 total tags in treatment: 15022820 INFO @ Tue, 30 Jun 2020 02:17:25: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:17:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:17:26: #1 tags after filtering in treatment: 15022818 INFO @ Tue, 30 Jun 2020 02:17:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:17:26: #1 finished! INFO @ Tue, 30 Jun 2020 02:17:26: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:17:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:17:27: #2 number of paired peaks: 696 WARNING @ Tue, 30 Jun 2020 02:17:27: Fewer paired peaks (696) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 696 pairs to build model! INFO @ Tue, 30 Jun 2020 02:17:27: start model_add_line... INFO @ Tue, 30 Jun 2020 02:17:27: start X-correlation... INFO @ Tue, 30 Jun 2020 02:17:27: end of X-cor INFO @ Tue, 30 Jun 2020 02:17:27: #2 finished! INFO @ Tue, 30 Jun 2020 02:17:27: #2 predicted fragment length is 39 bps INFO @ Tue, 30 Jun 2020 02:17:27: #2 alternative fragment length(s) may be 3,39 bps INFO @ Tue, 30 Jun 2020 02:17:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287973/SRX287973.20_model.r WARNING @ Tue, 30 Jun 2020 02:17:27: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:17:27: #2 You may need to consider one of the other alternative d(s): 3,39 WARNING @ Tue, 30 Jun 2020 02:17:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:17:27: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:17:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:17:31: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:17:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287973/SRX287973.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:17:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287973/SRX287973.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:17:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287973/SRX287973.10_summits.bed INFO @ Tue, 30 Jun 2020 02:17:45: Done! pass1 - making usageList (576 chroms): 2 millis pass2 - checking and writing primary data (2117 records, 4 fields): 33 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:17:53: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:18:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287973/SRX287973.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:18:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287973/SRX287973.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:18:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287973/SRX287973.20_summits.bed INFO @ Tue, 30 Jun 2020 02:18:07: Done! pass1 - making usageList (394 chroms): 1 millis pass2 - checking and writing primary data (1071 records, 4 fields): 23 millis CompletedMACS2peakCalling