Job ID = 14171101 SRX = SRX9063531 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 16338082 spots for SRR12576656/SRR12576656.sra Written 16338082 spots for SRR12576656/SRR12576656.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171560 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:38 16338082 reads; of these: 16338082 (100.00%) were unpaired; of these: 584152 (3.58%) aligned 0 times 11892487 (72.79%) aligned exactly 1 time 3861443 (23.63%) aligned >1 times 96.42% overall alignment rate Time searching: 00:07:38 Overall time: 00:07:38 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 4649897 / 15753930 = 0.2952 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 09:45:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9063531/SRX9063531.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9063531/SRX9063531.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9063531/SRX9063531.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9063531/SRX9063531.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, 11 Dec 2021 09:45:43: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:45:43: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:45:49: 1000000 INFO @ Sat, 11 Dec 2021 09:45:55: 2000000 INFO @ Sat, 11 Dec 2021 09:46:01: 3000000 INFO @ Sat, 11 Dec 2021 09:46:07: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 09:46:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9063531/SRX9063531.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9063531/SRX9063531.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9063531/SRX9063531.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9063531/SRX9063531.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, 11 Dec 2021 09:46:11: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:46:11: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:46:13: 5000000 INFO @ Sat, 11 Dec 2021 09:46:17: 1000000 INFO @ Sat, 11 Dec 2021 09:46:19: 6000000 INFO @ Sat, 11 Dec 2021 09:46:23: 2000000 INFO @ Sat, 11 Dec 2021 09:46:25: 7000000 INFO @ Sat, 11 Dec 2021 09:46:28: 3000000 INFO @ Sat, 11 Dec 2021 09:46:30: 8000000 INFO @ Sat, 11 Dec 2021 09:46:33: 4000000 INFO @ Sat, 11 Dec 2021 09:46:36: 9000000 INFO @ Sat, 11 Dec 2021 09:46:39: 5000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 09:46:41: 10000000 INFO @ Sat, 11 Dec 2021 09:46:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9063531/SRX9063531.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9063531/SRX9063531.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9063531/SRX9063531.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9063531/SRX9063531.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, 11 Dec 2021 09:46:41: #1 read tag files... INFO @ Sat, 11 Dec 2021 09:46:41: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 09:46:44: 6000000 INFO @ Sat, 11 Dec 2021 09:46:46: 11000000 INFO @ Sat, 11 Dec 2021 09:46:47: #1 tag size is determined as 76 bps INFO @ Sat, 11 Dec 2021 09:46:47: #1 tag size = 76 INFO @ Sat, 11 Dec 2021 09:46:47: #1 total tags in treatment: 11104033 INFO @ Sat, 11 Dec 2021 09:46:47: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:46:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 09:46:47: #1 tags after filtering in treatment: 11104033 INFO @ Sat, 11 Dec 2021 09:46:47: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:46:47: #1 finished! INFO @ Sat, 11 Dec 2021 09:46:47: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:46:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:46:48: #2 number of paired peaks: 106 WARNING @ Sat, 11 Dec 2021 09:46:48: Fewer paired peaks (106) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 106 pairs to build model! INFO @ Sat, 11 Dec 2021 09:46:48: start model_add_line... INFO @ Sat, 11 Dec 2021 09:46:48: start X-correlation... INFO @ Sat, 11 Dec 2021 09:46:48: end of X-cor INFO @ Sat, 11 Dec 2021 09:46:48: #2 finished! INFO @ Sat, 11 Dec 2021 09:46:48: #2 predicted fragment length is 87 bps INFO @ Sat, 11 Dec 2021 09:46:48: #2 alternative fragment length(s) may be 87 bps INFO @ Sat, 11 Dec 2021 09:46:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9063531/SRX9063531.05_model.r WARNING @ Sat, 11 Dec 2021 09:46:48: #2 Since the d (87) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:46:48: #2 You may need to consider one of the other alternative d(s): 87 WARNING @ Sat, 11 Dec 2021 09:46:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 09:46:48: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:46:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:46:50: 7000000 INFO @ Sat, 11 Dec 2021 09:46:51: 1000000 INFO @ Sat, 11 Dec 2021 09:46:55: 8000000 INFO @ Sat, 11 Dec 2021 09:47:00: 9000000 INFO @ Sat, 11 Dec 2021 09:47:01: 2000000 INFO @ Sat, 11 Dec 2021 09:47:06: 10000000 INFO @ Sat, 11 Dec 2021 09:47:10: 3000000 INFO @ Sat, 11 Dec 2021 09:47:11: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:47:11: 11000000 INFO @ Sat, 11 Dec 2021 09:47:12: #1 tag size is determined as 76 bps INFO @ Sat, 11 Dec 2021 09:47:12: #1 tag size = 76 INFO @ Sat, 11 Dec 2021 09:47:12: #1 total tags in treatment: 11104033 INFO @ Sat, 11 Dec 2021 09:47:12: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:47:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 09:47:12: #1 tags after filtering in treatment: 11104033 INFO @ Sat, 11 Dec 2021 09:47:12: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:47:12: #1 finished! INFO @ Sat, 11 Dec 2021 09:47:12: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:47:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:47:13: #2 number of paired peaks: 106 WARNING @ Sat, 11 Dec 2021 09:47:13: Fewer paired peaks (106) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 106 pairs to build model! INFO @ Sat, 11 Dec 2021 09:47:13: start model_add_line... INFO @ Sat, 11 Dec 2021 09:47:13: start X-correlation... INFO @ Sat, 11 Dec 2021 09:47:13: end of X-cor INFO @ Sat, 11 Dec 2021 09:47:13: #2 finished! INFO @ Sat, 11 Dec 2021 09:47:13: #2 predicted fragment length is 87 bps INFO @ Sat, 11 Dec 2021 09:47:13: #2 alternative fragment length(s) may be 87 bps INFO @ Sat, 11 Dec 2021 09:47:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9063531/SRX9063531.10_model.r WARNING @ Sat, 11 Dec 2021 09:47:13: #2 Since the d (87) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:47:13: #2 You may need to consider one of the other alternative d(s): 87 WARNING @ Sat, 11 Dec 2021 09:47:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 09:47:13: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:47:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 09:47:18: 4000000 INFO @ Sat, 11 Dec 2021 09:47:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9063531/SRX9063531.05_peaks.xls INFO @ Sat, 11 Dec 2021 09:47:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9063531/SRX9063531.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:47:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9063531/SRX9063531.05_summits.bed INFO @ Sat, 11 Dec 2021 09:47:22: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1217 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 09:47:27: 5000000 INFO @ Sat, 11 Dec 2021 09:47:35: 6000000 INFO @ Sat, 11 Dec 2021 09:47:35: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:47:43: 7000000 INFO @ Sat, 11 Dec 2021 09:47:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9063531/SRX9063531.10_peaks.xls INFO @ Sat, 11 Dec 2021 09:47:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9063531/SRX9063531.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:47:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9063531/SRX9063531.10_summits.bed INFO @ Sat, 11 Dec 2021 09:47:46: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (847 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 09:47:51: 8000000 INFO @ Sat, 11 Dec 2021 09:48:00: 9000000 INFO @ Sat, 11 Dec 2021 09:48:07: 10000000 INFO @ Sat, 11 Dec 2021 09:48:14: 11000000 INFO @ Sat, 11 Dec 2021 09:48:15: #1 tag size is determined as 76 bps INFO @ Sat, 11 Dec 2021 09:48:15: #1 tag size = 76 INFO @ Sat, 11 Dec 2021 09:48:15: #1 total tags in treatment: 11104033 INFO @ Sat, 11 Dec 2021 09:48:15: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 09:48:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 09:48:16: #1 tags after filtering in treatment: 11104033 INFO @ Sat, 11 Dec 2021 09:48:16: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 09:48:16: #1 finished! INFO @ Sat, 11 Dec 2021 09:48:16: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 09:48:16: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 09:48:17: #2 number of paired peaks: 106 WARNING @ Sat, 11 Dec 2021 09:48:17: Fewer paired peaks (106) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 106 pairs to build model! INFO @ Sat, 11 Dec 2021 09:48:17: start model_add_line... INFO @ Sat, 11 Dec 2021 09:48:17: start X-correlation... INFO @ Sat, 11 Dec 2021 09:48:17: end of X-cor INFO @ Sat, 11 Dec 2021 09:48:17: #2 finished! INFO @ Sat, 11 Dec 2021 09:48:17: #2 predicted fragment length is 87 bps INFO @ Sat, 11 Dec 2021 09:48:17: #2 alternative fragment length(s) may be 87 bps INFO @ Sat, 11 Dec 2021 09:48:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9063531/SRX9063531.20_model.r WARNING @ Sat, 11 Dec 2021 09:48:17: #2 Since the d (87) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 09:48:17: #2 You may need to consider one of the other alternative d(s): 87 WARNING @ Sat, 11 Dec 2021 09:48:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 09:48:17: #3 Call peaks... INFO @ Sat, 11 Dec 2021 09:48:17: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 09:48:45: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 09:49:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9063531/SRX9063531.20_peaks.xls INFO @ Sat, 11 Dec 2021 09:49:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9063531/SRX9063531.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 09:49:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9063531/SRX9063531.20_summits.bed INFO @ Sat, 11 Dec 2021 09:49:00: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (481 records, 4 fields): 1 millis CompletedMACS2peakCalling