Job ID = 12265439 SRX = SRX5010735 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: 00:10:07 41645070 reads; of these: 41645070 (100.00%) were unpaired; of these: 1258500 (3.02%) aligned 0 times 35478245 (85.19%) aligned exactly 1 time 4908325 (11.79%) aligned >1 times 96.98% overall alignment rate Time searching: 00:10:07 Overall time: 00:10:07 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] 29638619 / 40386570 = 0.7339 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 07:18:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5010735/SRX5010735.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5010735/SRX5010735.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5010735/SRX5010735.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5010735/SRX5010735.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 07:18:23: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:18:23: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:18:30: 1000000 INFO @ Sat, 03 Apr 2021 07:18:37: 2000000 INFO @ Sat, 03 Apr 2021 07:18:44: 3000000 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 07:18:50: 4000000 INFO @ Sat, 03 Apr 2021 07:18:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5010735/SRX5010735.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5010735/SRX5010735.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5010735/SRX5010735.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5010735/SRX5010735.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 07:18:51: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:18:51: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:18:57: 5000000 INFO @ Sat, 03 Apr 2021 07:18:58: 1000000 INFO @ Sat, 03 Apr 2021 07:19:03: 6000000 INFO @ Sat, 03 Apr 2021 07:19:05: 2000000 INFO @ Sat, 03 Apr 2021 07:19:09: 7000000 INFO @ Sat, 03 Apr 2021 07:19:12: 3000000 INFO @ Sat, 03 Apr 2021 07:19:16: 8000000 BedGraph に変換中... INFO @ Sat, 03 Apr 2021 07:19:19: 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 07:19:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5010735/SRX5010735.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5010735/SRX5010735.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5010735/SRX5010735.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5010735/SRX5010735.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 07:19:22: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:19:22: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:19:23: 9000000 INFO @ Sat, 03 Apr 2021 07:19:26: 5000000 INFO @ Sat, 03 Apr 2021 07:19:29: 1000000 INFO @ Sat, 03 Apr 2021 07:19:30: 10000000 INFO @ Sat, 03 Apr 2021 07:19:33: 6000000 INFO @ Sat, 03 Apr 2021 07:19:35: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 07:19:35: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 07:19:35: #1 total tags in treatment: 10747951 INFO @ Sat, 03 Apr 2021 07:19:35: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:19:35: #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 07:19:36: #1 tags after filtering in treatment: 10747864 INFO @ Sat, 03 Apr 2021 07:19:36: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 07:19:36: #1 finished! INFO @ Sat, 03 Apr 2021 07:19:36: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:19:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:19:36: 2000000 INFO @ Sat, 03 Apr 2021 07:19:37: #2 number of paired peaks: 682 WARNING @ Sat, 03 Apr 2021 07:19:37: Fewer paired peaks (682) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 682 pairs to build model! INFO @ Sat, 03 Apr 2021 07:19:37: start model_add_line... INFO @ Sat, 03 Apr 2021 07:19:37: start X-correlation... INFO @ Sat, 03 Apr 2021 07:19:37: end of X-cor INFO @ Sat, 03 Apr 2021 07:19:37: #2 finished! INFO @ Sat, 03 Apr 2021 07:19:37: #2 predicted fragment length is 52 bps INFO @ Sat, 03 Apr 2021 07:19:37: #2 alternative fragment length(s) may be 4,52 bps INFO @ Sat, 03 Apr 2021 07:19:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5010735/SRX5010735.05_model.r WARNING @ Sat, 03 Apr 2021 07:19:37: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:19:37: #2 You may need to consider one of the other alternative d(s): 4,52 WARNING @ Sat, 03 Apr 2021 07:19:37: #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 07:19:37: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:19:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:19:40: 7000000 INFO @ Sat, 03 Apr 2021 07:19:43: 3000000 INFO @ Sat, 03 Apr 2021 07:19:47: 8000000 INFO @ Sat, 03 Apr 2021 07:19:50: 4000000 INFO @ Sat, 03 Apr 2021 07:19:54: 9000000 INFO @ Sat, 03 Apr 2021 07:19:58: 5000000 INFO @ Sat, 03 Apr 2021 07:20:01: 10000000 INFO @ Sat, 03 Apr 2021 07:20:04: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:20:05: 6000000 INFO @ Sat, 03 Apr 2021 07:20:06: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 07:20:06: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 07:20:06: #1 total tags in treatment: 10747951 INFO @ Sat, 03 Apr 2021 07:20:06: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:20:06: #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 07:20:07: #1 tags after filtering in treatment: 10747864 INFO @ Sat, 03 Apr 2021 07:20:07: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 07:20:07: #1 finished! INFO @ Sat, 03 Apr 2021 07:20:07: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:20:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:20:08: #2 number of paired peaks: 682 WARNING @ Sat, 03 Apr 2021 07:20:08: Fewer paired peaks (682) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 682 pairs to build model! INFO @ Sat, 03 Apr 2021 07:20:08: start model_add_line... INFO @ Sat, 03 Apr 2021 07:20:08: start X-correlation... INFO @ Sat, 03 Apr 2021 07:20:08: end of X-cor INFO @ Sat, 03 Apr 2021 07:20:08: #2 finished! INFO @ Sat, 03 Apr 2021 07:20:08: #2 predicted fragment length is 52 bps INFO @ Sat, 03 Apr 2021 07:20:08: #2 alternative fragment length(s) may be 4,52 bps INFO @ Sat, 03 Apr 2021 07:20:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5010735/SRX5010735.10_model.r WARNING @ Sat, 03 Apr 2021 07:20:08: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:20:08: #2 You may need to consider one of the other alternative d(s): 4,52 WARNING @ Sat, 03 Apr 2021 07:20:08: #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 07:20:08: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:20:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:20:12: 7000000 INFO @ Sat, 03 Apr 2021 07:20:18: 8000000 INFO @ Sat, 03 Apr 2021 07:20:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5010735/SRX5010735.05_peaks.xls INFO @ Sat, 03 Apr 2021 07:20:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5010735/SRX5010735.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:20:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5010735/SRX5010735.05_summits.bed INFO @ Sat, 03 Apr 2021 07:20:19: Done! pass1 - making usageList (420 chroms): 12 millis pass2 - checking and writing primary data (5447 records, 4 fields): 50 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 07:20:26: 9000000 INFO @ Sat, 03 Apr 2021 07:20:32: 10000000 INFO @ Sat, 03 Apr 2021 07:20:36: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:20:38: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 07:20:38: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 07:20:38: #1 total tags in treatment: 10747951 INFO @ Sat, 03 Apr 2021 07:20:38: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:20:38: #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 07:20:38: #1 tags after filtering in treatment: 10747864 INFO @ Sat, 03 Apr 2021 07:20:38: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 07:20:38: #1 finished! INFO @ Sat, 03 Apr 2021 07:20:38: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:20:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:20:39: #2 number of paired peaks: 682 WARNING @ Sat, 03 Apr 2021 07:20:39: Fewer paired peaks (682) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 682 pairs to build model! INFO @ Sat, 03 Apr 2021 07:20:39: start model_add_line... INFO @ Sat, 03 Apr 2021 07:20:39: start X-correlation... INFO @ Sat, 03 Apr 2021 07:20:39: end of X-cor INFO @ Sat, 03 Apr 2021 07:20:39: #2 finished! INFO @ Sat, 03 Apr 2021 07:20:39: #2 predicted fragment length is 52 bps INFO @ Sat, 03 Apr 2021 07:20:39: #2 alternative fragment length(s) may be 4,52 bps INFO @ Sat, 03 Apr 2021 07:20:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5010735/SRX5010735.20_model.r WARNING @ Sat, 03 Apr 2021 07:20:39: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:20:39: #2 You may need to consider one of the other alternative d(s): 4,52 WARNING @ Sat, 03 Apr 2021 07:20:39: #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 07:20:39: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:20:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:20:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5010735/SRX5010735.10_peaks.xls INFO @ Sat, 03 Apr 2021 07:20:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5010735/SRX5010735.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:20:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5010735/SRX5010735.10_summits.bed INFO @ Sat, 03 Apr 2021 07:20:50: Done! pass1 - making usageList (203 chroms): 23 millis pass2 - checking and writing primary data (1753 records, 4 fields): 53 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 07:21:06: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:21:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5010735/SRX5010735.20_peaks.xls INFO @ Sat, 03 Apr 2021 07:21:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5010735/SRX5010735.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:21:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5010735/SRX5010735.20_summits.bed INFO @ Sat, 03 Apr 2021 07:21:20: Done! pass1 - making usageList (118 chroms): 12 millis pass2 - checking and writing primary data (389 records, 4 fields): 28 millis CompletedMACS2peakCalling