Job ID = 12265470 SRX = SRX5010743 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: 00:00:00 Multiseed full-index search: 00:11:54 47304001 reads; of these: 47304001 (100.00%) were unpaired; of these: 1617540 (3.42%) aligned 0 times 38296004 (80.96%) aligned exactly 1 time 7390457 (15.62%) aligned >1 times 96.58% overall alignment rate Time searching: 00:11:54 Overall time: 00:11:54 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 20 files... [bam_rmdupse_core] 30643886 / 45686461 = 0.6707 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 07:31:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5010743/SRX5010743.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5010743/SRX5010743.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5010743/SRX5010743.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5010743/SRX5010743.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 07:31:29: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:31:29: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:31:36: 1000000 INFO @ Sat, 03 Apr 2021 07:31:43: 2000000 INFO @ Sat, 03 Apr 2021 07:31:49: 3000000 INFO @ Sat, 03 Apr 2021 07:31:56: 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 07:31:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5010743/SRX5010743.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5010743/SRX5010743.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5010743/SRX5010743.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5010743/SRX5010743.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 07:31:59: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:31:59: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:32:02: 5000000 INFO @ Sat, 03 Apr 2021 07:32:07: 1000000 INFO @ Sat, 03 Apr 2021 07:32:10: 6000000 INFO @ Sat, 03 Apr 2021 07:32:15: 2000000 INFO @ Sat, 03 Apr 2021 07:32:17: 7000000 INFO @ Sat, 03 Apr 2021 07:32:23: 3000000 INFO @ Sat, 03 Apr 2021 07:32:25: 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 07:32:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5010743/SRX5010743.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5010743/SRX5010743.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5010743/SRX5010743.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5010743/SRX5010743.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 07:32:29: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:32:29: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:32:30: 4000000 INFO @ Sat, 03 Apr 2021 07:32:33: 9000000 INFO @ Sat, 03 Apr 2021 07:32:37: 1000000 INFO @ Sat, 03 Apr 2021 07:32:38: 5000000 INFO @ Sat, 03 Apr 2021 07:32:41: 10000000 INFO @ Sat, 03 Apr 2021 07:32:45: 2000000 INFO @ Sat, 03 Apr 2021 07:32:46: 6000000 INFO @ Sat, 03 Apr 2021 07:32:49: 11000000 INFO @ Sat, 03 Apr 2021 07:32:53: 3000000 INFO @ Sat, 03 Apr 2021 07:32:54: 7000000 INFO @ Sat, 03 Apr 2021 07:32:57: 12000000 INFO @ Sat, 03 Apr 2021 07:33:01: 4000000 INFO @ Sat, 03 Apr 2021 07:33:02: 8000000 INFO @ Sat, 03 Apr 2021 07:33:05: 13000000 INFO @ Sat, 03 Apr 2021 07:33:09: 5000000 INFO @ Sat, 03 Apr 2021 07:33:10: 9000000 INFO @ Sat, 03 Apr 2021 07:33:14: 14000000 INFO @ Sat, 03 Apr 2021 07:33:17: 6000000 INFO @ Sat, 03 Apr 2021 07:33:19: 10000000 INFO @ Sat, 03 Apr 2021 07:33:22: 15000000 INFO @ Sat, 03 Apr 2021 07:33:23: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 07:33:23: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 07:33:23: #1 total tags in treatment: 15042575 INFO @ Sat, 03 Apr 2021 07:33:23: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:33:23: #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 07:33:24: #1 tags after filtering in treatment: 15042504 INFO @ Sat, 03 Apr 2021 07:33:24: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 07:33:24: #1 finished! INFO @ Sat, 03 Apr 2021 07:33:24: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:33:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:33:25: #2 number of paired peaks: 487 WARNING @ Sat, 03 Apr 2021 07:33:25: Fewer paired peaks (487) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 487 pairs to build model! INFO @ Sat, 03 Apr 2021 07:33:25: start model_add_line... INFO @ Sat, 03 Apr 2021 07:33:25: start X-correlation... INFO @ Sat, 03 Apr 2021 07:33:25: end of X-cor INFO @ Sat, 03 Apr 2021 07:33:25: #2 finished! INFO @ Sat, 03 Apr 2021 07:33:25: #2 predicted fragment length is 51 bps INFO @ Sat, 03 Apr 2021 07:33:25: #2 alternative fragment length(s) may be 4,51 bps INFO @ Sat, 03 Apr 2021 07:33:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5010743/SRX5010743.05_model.r WARNING @ Sat, 03 Apr 2021 07:33:25: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:33:25: #2 You may need to consider one of the other alternative d(s): 4,51 WARNING @ Sat, 03 Apr 2021 07:33:25: #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 07:33:25: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:33:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:33:26: 7000000 INFO @ Sat, 03 Apr 2021 07:33:27: 11000000 INFO @ Sat, 03 Apr 2021 07:33:34: 8000000 INFO @ Sat, 03 Apr 2021 07:33:36: 12000000 INFO @ Sat, 03 Apr 2021 07:33:42: 9000000 INFO @ Sat, 03 Apr 2021 07:33:45: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 07:33:51: 10000000 INFO @ Sat, 03 Apr 2021 07:33:52: 14000000 INFO @ Sat, 03 Apr 2021 07:33:55: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:33:59: 11000000 INFO @ Sat, 03 Apr 2021 07:34:00: 15000000 INFO @ Sat, 03 Apr 2021 07:34:00: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 07:34:00: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 07:34:00: #1 total tags in treatment: 15042575 INFO @ Sat, 03 Apr 2021 07:34:00: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:34:00: #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 07:34:01: #1 tags after filtering in treatment: 15042504 INFO @ Sat, 03 Apr 2021 07:34:01: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 07:34:01: #1 finished! INFO @ Sat, 03 Apr 2021 07:34:01: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:34:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:34:02: #2 number of paired peaks: 487 WARNING @ Sat, 03 Apr 2021 07:34:02: Fewer paired peaks (487) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 487 pairs to build model! INFO @ Sat, 03 Apr 2021 07:34:02: start model_add_line... INFO @ Sat, 03 Apr 2021 07:34:02: start X-correlation... INFO @ Sat, 03 Apr 2021 07:34:02: end of X-cor INFO @ Sat, 03 Apr 2021 07:34:02: #2 finished! INFO @ Sat, 03 Apr 2021 07:34:02: #2 predicted fragment length is 51 bps INFO @ Sat, 03 Apr 2021 07:34:02: #2 alternative fragment length(s) may be 4,51 bps INFO @ Sat, 03 Apr 2021 07:34:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5010743/SRX5010743.10_model.r WARNING @ Sat, 03 Apr 2021 07:34:02: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:34:02: #2 You may need to consider one of the other alternative d(s): 4,51 WARNING @ Sat, 03 Apr 2021 07:34:02: #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 07:34:02: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:34:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:34:07: 12000000 INFO @ Sat, 03 Apr 2021 07:34:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5010743/SRX5010743.05_peaks.xls INFO @ Sat, 03 Apr 2021 07:34:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5010743/SRX5010743.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:34:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5010743/SRX5010743.05_summits.bed INFO @ Sat, 03 Apr 2021 07:34:12: Done! pass1 - making usageList (554 chroms): 3 millis pass2 - checking and writing primary data (9632 records, 4 fields): 42 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:34:15: 13000000 INFO @ Sat, 03 Apr 2021 07:34:23: 14000000 INFO @ Sat, 03 Apr 2021 07:34:30: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:34:32: 15000000 BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 07:34:32: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 07:34:32: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 07:34:32: #1 total tags in treatment: 15042575 INFO @ Sat, 03 Apr 2021 07:34:32: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:34:32: #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 07:34:33: #1 tags after filtering in treatment: 15042504 INFO @ Sat, 03 Apr 2021 07:34:33: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 07:34:33: #1 finished! INFO @ Sat, 03 Apr 2021 07:34:33: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:34:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:34:34: #2 number of paired peaks: 487 WARNING @ Sat, 03 Apr 2021 07:34:34: Fewer paired peaks (487) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 487 pairs to build model! INFO @ Sat, 03 Apr 2021 07:34:34: start model_add_line... INFO @ Sat, 03 Apr 2021 07:34:34: start X-correlation... INFO @ Sat, 03 Apr 2021 07:34:34: end of X-cor INFO @ Sat, 03 Apr 2021 07:34:34: #2 finished! INFO @ Sat, 03 Apr 2021 07:34:34: #2 predicted fragment length is 51 bps INFO @ Sat, 03 Apr 2021 07:34:34: #2 alternative fragment length(s) may be 4,51 bps INFO @ Sat, 03 Apr 2021 07:34:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5010743/SRX5010743.20_model.r WARNING @ Sat, 03 Apr 2021 07:34:34: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:34:34: #2 You may need to consider one of the other alternative d(s): 4,51 WARNING @ Sat, 03 Apr 2021 07:34:34: #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 07:34:34: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:34:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:34:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5010743/SRX5010743.10_peaks.xls INFO @ Sat, 03 Apr 2021 07:34:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5010743/SRX5010743.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:34:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5010743/SRX5010743.10_summits.bed INFO @ Sat, 03 Apr 2021 07:34:45: Done! pass1 - making usageList (297 chroms): 1 millis pass2 - checking and writing primary data (3209 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:35:03: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:35:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5010743/SRX5010743.20_peaks.xls INFO @ Sat, 03 Apr 2021 07:35:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5010743/SRX5010743.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:35:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5010743/SRX5010743.20_summits.bed INFO @ Sat, 03 Apr 2021 07:35:19: Done! pass1 - making usageList (131 chroms): 1 millis pass2 - checking and writing primary data (527 records, 4 fields): 10 millis CompletedMACS2peakCalling