Job ID = 6529604 SRX = SRX3380791 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: 00:04:10 14950163 reads; of these: 14950163 (100.00%) were unpaired; of these: 586115 (3.92%) aligned 0 times 11128371 (74.44%) aligned exactly 1 time 3235677 (21.64%) aligned >1 times 96.08% overall alignment rate Time searching: 00:04:11 Overall time: 00:04:11 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] 1362240 / 14364048 = 0.0948 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 02:33:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3380791/SRX3380791.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3380791/SRX3380791.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3380791/SRX3380791.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3380791/SRX3380791.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 02:33:11: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:33:11: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:33:17: 1000000 INFO @ Tue, 30 Jun 2020 02:33:23: 2000000 INFO @ Tue, 30 Jun 2020 02:33:29: 3000000 INFO @ Tue, 30 Jun 2020 02:33:35: 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 02:33:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3380791/SRX3380791.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3380791/SRX3380791.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3380791/SRX3380791.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3380791/SRX3380791.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 02:33:41: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:33:41: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:33:42: 5000000 INFO @ Tue, 30 Jun 2020 02:33:47: 1000000 INFO @ Tue, 30 Jun 2020 02:33:49: 6000000 INFO @ Tue, 30 Jun 2020 02:33:54: 2000000 INFO @ Tue, 30 Jun 2020 02:33:55: 7000000 INFO @ Tue, 30 Jun 2020 02:34:00: 3000000 INFO @ Tue, 30 Jun 2020 02:34:02: 8000000 INFO @ Tue, 30 Jun 2020 02:34:06: 4000000 INFO @ Tue, 30 Jun 2020 02:34:08: 9000000 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 02:34:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3380791/SRX3380791.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3380791/SRX3380791.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3380791/SRX3380791.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3380791/SRX3380791.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 02:34:11: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:34:11: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:34:13: 5000000 INFO @ Tue, 30 Jun 2020 02:34:15: 10000000 INFO @ Tue, 30 Jun 2020 02:34:18: 1000000 INFO @ Tue, 30 Jun 2020 02:34:20: 6000000 INFO @ Tue, 30 Jun 2020 02:34:22: 11000000 INFO @ Tue, 30 Jun 2020 02:34:24: 2000000 INFO @ Tue, 30 Jun 2020 02:34:26: 7000000 INFO @ Tue, 30 Jun 2020 02:34:29: 12000000 INFO @ Tue, 30 Jun 2020 02:34:30: 3000000 INFO @ Tue, 30 Jun 2020 02:34:32: 8000000 INFO @ Tue, 30 Jun 2020 02:34:36: 13000000 INFO @ Tue, 30 Jun 2020 02:34:36: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:34:36: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:34:36: #1 total tags in treatment: 13001808 INFO @ Tue, 30 Jun 2020 02:34:36: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:34:36: #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 02:34:36: #1 tags after filtering in treatment: 13001803 INFO @ Tue, 30 Jun 2020 02:34:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:34:36: #1 finished! INFO @ Tue, 30 Jun 2020 02:34:36: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:34:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:34:37: 4000000 INFO @ Tue, 30 Jun 2020 02:34:37: #2 number of paired peaks: 198 WARNING @ Tue, 30 Jun 2020 02:34:37: Fewer paired peaks (198) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 198 pairs to build model! INFO @ Tue, 30 Jun 2020 02:34:37: start model_add_line... INFO @ Tue, 30 Jun 2020 02:34:37: start X-correlation... INFO @ Tue, 30 Jun 2020 02:34:37: end of X-cor INFO @ Tue, 30 Jun 2020 02:34:37: #2 finished! INFO @ Tue, 30 Jun 2020 02:34:37: #2 predicted fragment length is 95 bps INFO @ Tue, 30 Jun 2020 02:34:37: #2 alternative fragment length(s) may be 95 bps INFO @ Tue, 30 Jun 2020 02:34:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3380791/SRX3380791.05_model.r WARNING @ Tue, 30 Jun 2020 02:34:37: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:34:37: #2 You may need to consider one of the other alternative d(s): 95 WARNING @ Tue, 30 Jun 2020 02:34:37: #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 02:34:37: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:34:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:34:39: 9000000 INFO @ Tue, 30 Jun 2020 02:34:43: 5000000 INFO @ Tue, 30 Jun 2020 02:34:45: 10000000 INFO @ Tue, 30 Jun 2020 02:34:50: 6000000 INFO @ Tue, 30 Jun 2020 02:34:52: 11000000 INFO @ Tue, 30 Jun 2020 02:34:57: 7000000 INFO @ Tue, 30 Jun 2020 02:34:59: 12000000 INFO @ Tue, 30 Jun 2020 02:35:03: 8000000 INFO @ Tue, 30 Jun 2020 02:35:06: 13000000 INFO @ Tue, 30 Jun 2020 02:35:06: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:35:06: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:35:06: #1 total tags in treatment: 13001808 INFO @ Tue, 30 Jun 2020 02:35:06: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:35:06: #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 02:35:07: #1 tags after filtering in treatment: 13001803 INFO @ Tue, 30 Jun 2020 02:35:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:35:07: #1 finished! INFO @ Tue, 30 Jun 2020 02:35:07: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:35:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:35:07: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:35:08: #2 number of paired peaks: 198 WARNING @ Tue, 30 Jun 2020 02:35:08: Fewer paired peaks (198) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 198 pairs to build model! INFO @ Tue, 30 Jun 2020 02:35:08: start model_add_line... INFO @ Tue, 30 Jun 2020 02:35:08: start X-correlation... INFO @ Tue, 30 Jun 2020 02:35:08: end of X-cor INFO @ Tue, 30 Jun 2020 02:35:08: #2 finished! INFO @ Tue, 30 Jun 2020 02:35:08: #2 predicted fragment length is 95 bps INFO @ Tue, 30 Jun 2020 02:35:08: #2 alternative fragment length(s) may be 95 bps INFO @ Tue, 30 Jun 2020 02:35:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3380791/SRX3380791.10_model.r WARNING @ Tue, 30 Jun 2020 02:35:08: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:35:08: #2 You may need to consider one of the other alternative d(s): 95 WARNING @ Tue, 30 Jun 2020 02:35:08: #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 02:35:08: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:35:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:35:10: 9000000 INFO @ Tue, 30 Jun 2020 02:35:16: 10000000 INFO @ Tue, 30 Jun 2020 02:35:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3380791/SRX3380791.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:35:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3380791/SRX3380791.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:35:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3380791/SRX3380791.05_summits.bed INFO @ Tue, 30 Jun 2020 02:35:23: Done! pass1 - making usageList (526 chroms): 1 millis pass2 - checking and writing primary data (1697 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:35:23: 11000000 INFO @ Tue, 30 Jun 2020 02:35:30: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:35:37: 13000000 INFO @ Tue, 30 Jun 2020 02:35:37: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:35:37: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:35:37: #1 total tags in treatment: 13001808 INFO @ Tue, 30 Jun 2020 02:35:37: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:35:37: #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 02:35:38: #1 tags after filtering in treatment: 13001803 INFO @ Tue, 30 Jun 2020 02:35:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:35:38: #1 finished! INFO @ Tue, 30 Jun 2020 02:35:38: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:35:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:35:38: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:35:39: #2 number of paired peaks: 198 WARNING @ Tue, 30 Jun 2020 02:35:39: Fewer paired peaks (198) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 198 pairs to build model! INFO @ Tue, 30 Jun 2020 02:35:39: start model_add_line... INFO @ Tue, 30 Jun 2020 02:35:39: start X-correlation... INFO @ Tue, 30 Jun 2020 02:35:39: end of X-cor INFO @ Tue, 30 Jun 2020 02:35:39: #2 finished! INFO @ Tue, 30 Jun 2020 02:35:39: #2 predicted fragment length is 95 bps INFO @ Tue, 30 Jun 2020 02:35:39: #2 alternative fragment length(s) may be 95 bps INFO @ Tue, 30 Jun 2020 02:35:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3380791/SRX3380791.20_model.r WARNING @ Tue, 30 Jun 2020 02:35:39: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:35:39: #2 You may need to consider one of the other alternative d(s): 95 WARNING @ Tue, 30 Jun 2020 02:35:39: #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 02:35:39: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:35:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:35:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3380791/SRX3380791.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:35:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3380791/SRX3380791.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:35:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3380791/SRX3380791.10_summits.bed INFO @ Tue, 30 Jun 2020 02:35:53: Done! pass1 - making usageList (359 chroms): 1 millis pass2 - checking and writing primary data (836 records, 4 fields): 13 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:36:10: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:36:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3380791/SRX3380791.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:36:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3380791/SRX3380791.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:36:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3380791/SRX3380791.20_summits.bed INFO @ Tue, 30 Jun 2020 02:36:26: Done! pass1 - making usageList (140 chroms): 1 millis pass2 - checking and writing primary data (260 records, 4 fields): 7 millis CompletedMACS2peakCalling