Job ID = 12265435 SRX = SRX5010727 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: 00:09:18 38691516 reads; of these: 38691516 (100.00%) were unpaired; of these: 1369569 (3.54%) aligned 0 times 30814259 (79.64%) aligned exactly 1 time 6507688 (16.82%) aligned >1 times 96.46% overall alignment rate Time searching: 00:09:19 Overall time: 00:09:19 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 16 files... [bam_rmdupse_core] 22748740 / 37321947 = 0.6095 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:16:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5010727/SRX5010727.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5010727/SRX5010727.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5010727/SRX5010727.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5010727/SRX5010727.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 @ Sat, 03 Apr 2021 07:16:19: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:16:19: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:16:26: 1000000 INFO @ Sat, 03 Apr 2021 07:16:33: 2000000 INFO @ Sat, 03 Apr 2021 07:16:40: 3000000 INFO @ Sat, 03 Apr 2021 07:16:46: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:16:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5010727/SRX5010727.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5010727/SRX5010727.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5010727/SRX5010727.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5010727/SRX5010727.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 @ Sat, 03 Apr 2021 07:16:49: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:16:49: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:16:53: 5000000 INFO @ Sat, 03 Apr 2021 07:16:56: 1000000 INFO @ Sat, 03 Apr 2021 07:17:01: 6000000 INFO @ Sat, 03 Apr 2021 07:17:02: 2000000 INFO @ Sat, 03 Apr 2021 07:17:08: 7000000 INFO @ Sat, 03 Apr 2021 07:17:09: 3000000 INFO @ Sat, 03 Apr 2021 07:17:15: 4000000 INFO @ Sat, 03 Apr 2021 07:17:15: 8000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 07:17:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5010727/SRX5010727.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5010727/SRX5010727.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5010727/SRX5010727.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5010727/SRX5010727.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 @ Sat, 03 Apr 2021 07:17:19: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:17:19: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:17:22: 5000000 INFO @ Sat, 03 Apr 2021 07:17:23: 9000000 INFO @ Sat, 03 Apr 2021 07:17:26: 1000000 INFO @ Sat, 03 Apr 2021 07:17:29: 6000000 INFO @ Sat, 03 Apr 2021 07:17:30: 10000000 INFO @ Sat, 03 Apr 2021 07:17:33: 2000000 INFO @ Sat, 03 Apr 2021 07:17:35: 7000000 INFO @ Sat, 03 Apr 2021 07:17:38: 11000000 INFO @ Sat, 03 Apr 2021 07:17:40: 3000000 INFO @ Sat, 03 Apr 2021 07:17:42: 8000000 INFO @ Sat, 03 Apr 2021 07:17:45: 12000000 INFO @ Sat, 03 Apr 2021 07:17:47: 4000000 INFO @ Sat, 03 Apr 2021 07:17:49: 9000000 INFO @ Sat, 03 Apr 2021 07:17:53: 13000000 INFO @ Sat, 03 Apr 2021 07:17:54: 5000000 INFO @ Sat, 03 Apr 2021 07:17:56: 10000000 INFO @ Sat, 03 Apr 2021 07:18:00: 14000000 INFO @ Sat, 03 Apr 2021 07:18:00: 6000000 INFO @ Sat, 03 Apr 2021 07:18:03: 11000000 INFO @ Sat, 03 Apr 2021 07:18:04: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 07:18:04: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 07:18:04: #1 total tags in treatment: 14573207 INFO @ Sat, 03 Apr 2021 07:18:04: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:18:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:18:05: #1 tags after filtering in treatment: 14573141 INFO @ Sat, 03 Apr 2021 07:18:05: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 07:18:05: #1 finished! INFO @ Sat, 03 Apr 2021 07:18:05: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:18:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:18:06: #2 number of paired peaks: 515 WARNING @ Sat, 03 Apr 2021 07:18:06: Fewer paired peaks (515) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 515 pairs to build model! INFO @ Sat, 03 Apr 2021 07:18:06: start model_add_line... INFO @ Sat, 03 Apr 2021 07:18:06: start X-correlation... INFO @ Sat, 03 Apr 2021 07:18:06: end of X-cor INFO @ Sat, 03 Apr 2021 07:18:06: #2 finished! INFO @ Sat, 03 Apr 2021 07:18:06: #2 predicted fragment length is 62 bps INFO @ Sat, 03 Apr 2021 07:18:06: #2 alternative fragment length(s) may be 4,62 bps INFO @ Sat, 03 Apr 2021 07:18:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5010727/SRX5010727.05_model.r WARNING @ Sat, 03 Apr 2021 07:18:06: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:18:06: #2 You may need to consider one of the other alternative d(s): 4,62 WARNING @ Sat, 03 Apr 2021 07:18:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:18:06: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:18:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:18:07: 7000000 INFO @ Sat, 03 Apr 2021 07:18:10: 12000000 INFO @ Sat, 03 Apr 2021 07:18:14: 8000000 INFO @ Sat, 03 Apr 2021 07:18:16: 13000000 INFO @ Sat, 03 Apr 2021 07:18:20: 9000000 INFO @ Sat, 03 Apr 2021 07:18:23: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 07:18:27: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 07:18:27: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 07:18:27: #1 total tags in treatment: 14573207 INFO @ Sat, 03 Apr 2021 07:18:27: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:18:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:18:27: 10000000 INFO @ Sat, 03 Apr 2021 07:18:27: #1 tags after filtering in treatment: 14573141 INFO @ Sat, 03 Apr 2021 07:18:27: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 07:18:27: #1 finished! INFO @ Sat, 03 Apr 2021 07:18:27: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:18:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:18:28: #2 number of paired peaks: 515 WARNING @ Sat, 03 Apr 2021 07:18:28: Fewer paired peaks (515) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 515 pairs to build model! INFO @ Sat, 03 Apr 2021 07:18:28: start model_add_line... INFO @ Sat, 03 Apr 2021 07:18:28: start X-correlation... INFO @ Sat, 03 Apr 2021 07:18:28: end of X-cor INFO @ Sat, 03 Apr 2021 07:18:28: #2 finished! INFO @ Sat, 03 Apr 2021 07:18:28: #2 predicted fragment length is 62 bps INFO @ Sat, 03 Apr 2021 07:18:28: #2 alternative fragment length(s) may be 4,62 bps INFO @ Sat, 03 Apr 2021 07:18:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5010727/SRX5010727.10_model.r WARNING @ Sat, 03 Apr 2021 07:18:28: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:18:28: #2 You may need to consider one of the other alternative d(s): 4,62 WARNING @ Sat, 03 Apr 2021 07:18:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:18:28: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:18:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:18:33: 11000000 INFO @ Sat, 03 Apr 2021 07:18:39: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:18:39: 12000000 INFO @ Sat, 03 Apr 2021 07:18:45: 13000000 INFO @ Sat, 03 Apr 2021 07:18:50: 14000000 INFO @ Sat, 03 Apr 2021 07:18:53: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 07:18:53: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 07:18:53: #1 total tags in treatment: 14573207 INFO @ Sat, 03 Apr 2021 07:18:53: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:18:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 07:18:54: #1 tags after filtering in treatment: 14573141 INFO @ Sat, 03 Apr 2021 07:18:54: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 07:18:54: #1 finished! INFO @ Sat, 03 Apr 2021 07:18:54: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:18:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:18:55: #2 number of paired peaks: 515 WARNING @ Sat, 03 Apr 2021 07:18:55: Fewer paired peaks (515) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 515 pairs to build model! INFO @ Sat, 03 Apr 2021 07:18:55: start model_add_line... INFO @ Sat, 03 Apr 2021 07:18:55: start X-correlation... INFO @ Sat, 03 Apr 2021 07:18:55: end of X-cor INFO @ Sat, 03 Apr 2021 07:18:55: #2 finished! INFO @ Sat, 03 Apr 2021 07:18:55: #2 predicted fragment length is 62 bps INFO @ Sat, 03 Apr 2021 07:18:55: #2 alternative fragment length(s) may be 4,62 bps INFO @ Sat, 03 Apr 2021 07:18:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5010727/SRX5010727.20_model.r WARNING @ Sat, 03 Apr 2021 07:18:55: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:18:55: #2 You may need to consider one of the other alternative d(s): 4,62 WARNING @ Sat, 03 Apr 2021 07:18:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 07:18:55: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:18:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:18:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5010727/SRX5010727.05_peaks.xls INFO @ Sat, 03 Apr 2021 07:18:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5010727/SRX5010727.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:18:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5010727/SRX5010727.05_summits.bed INFO @ Sat, 03 Apr 2021 07:18:56: Done! BigWig に変換しました。 pass1 - making usageList (472 chroms): 2 millis pass2 - checking and writing primary data (10371 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:18:59: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:19:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5010727/SRX5010727.10_peaks.xls INFO @ Sat, 03 Apr 2021 07:19:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5010727/SRX5010727.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:19:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5010727/SRX5010727.10_summits.bed INFO @ Sat, 03 Apr 2021 07:19:14: Done! pass1 - making usageList (320 chroms): 1 millis pass2 - checking and writing primary data (4223 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:19:25: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:19:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5010727/SRX5010727.20_peaks.xls INFO @ Sat, 03 Apr 2021 07:19:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5010727/SRX5010727.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:19:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5010727/SRX5010727.20_summits.bed INFO @ Sat, 03 Apr 2021 07:19:41: Done! pass1 - making usageList (136 chroms): 1 millis pass2 - checking and writing primary data (903 records, 4 fields): 7 millis CompletedMACS2peakCalling