Job ID = 14172470 SRX = SRX7434134 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 16688735 spots for SRR10759900/SRR10759900.sra Written 16688735 spots for SRR10759900/SRR10759900.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172919 ("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: 00:05:25 16688735 reads; of these: 16688735 (100.00%) were unpaired; of these: 1217807 (7.30%) aligned 0 times 11091749 (66.46%) aligned exactly 1 time 4379179 (26.24%) aligned >1 times 92.70% overall alignment rate Time searching: 00:05:25 Overall time: 00:05:25 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] 1764684 / 15470928 = 0.1141 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 15:43:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7434134/SRX7434134.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7434134/SRX7434134.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7434134/SRX7434134.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7434134/SRX7434134.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 15:43:28: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:43:28: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:43:35: 1000000 INFO @ Sat, 11 Dec 2021 15:43:42: 2000000 INFO @ Sat, 11 Dec 2021 15:43:49: 3000000 INFO @ Sat, 11 Dec 2021 15:43:56: 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 15:43:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7434134/SRX7434134.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7434134/SRX7434134.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7434134/SRX7434134.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7434134/SRX7434134.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 15:43:58: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:43:58: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:44:03: 5000000 INFO @ Sat, 11 Dec 2021 15:44:04: 1000000 INFO @ Sat, 11 Dec 2021 15:44:10: 2000000 INFO @ Sat, 11 Dec 2021 15:44:11: 6000000 INFO @ Sat, 11 Dec 2021 15:44:15: 3000000 INFO @ Sat, 11 Dec 2021 15:44:19: 7000000 INFO @ Sat, 11 Dec 2021 15:44:21: 4000000 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 15:44:26: 8000000 INFO @ Sat, 11 Dec 2021 15:44:27: 5000000 INFO @ Sat, 11 Dec 2021 15:44:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7434134/SRX7434134.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7434134/SRX7434134.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7434134/SRX7434134.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7434134/SRX7434134.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 15:44:28: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:44:28: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:44:33: 6000000 INFO @ Sat, 11 Dec 2021 15:44:34: 9000000 INFO @ Sat, 11 Dec 2021 15:44:34: 1000000 INFO @ Sat, 11 Dec 2021 15:44:39: 7000000 INFO @ Sat, 11 Dec 2021 15:44:40: 2000000 INFO @ Sat, 11 Dec 2021 15:44:41: 10000000 INFO @ Sat, 11 Dec 2021 15:44:45: 8000000 INFO @ Sat, 11 Dec 2021 15:44:46: 3000000 INFO @ Sat, 11 Dec 2021 15:44:49: 11000000 INFO @ Sat, 11 Dec 2021 15:44:51: 9000000 INFO @ Sat, 11 Dec 2021 15:44:52: 4000000 INFO @ Sat, 11 Dec 2021 15:44:56: 12000000 INFO @ Sat, 11 Dec 2021 15:44:57: 10000000 INFO @ Sat, 11 Dec 2021 15:44:58: 5000000 INFO @ Sat, 11 Dec 2021 15:45:02: 13000000 INFO @ Sat, 11 Dec 2021 15:45:03: 11000000 INFO @ Sat, 11 Dec 2021 15:45:04: 6000000 INFO @ Sat, 11 Dec 2021 15:45:07: #1 tag size is determined as 51 bps INFO @ Sat, 11 Dec 2021 15:45:07: #1 tag size = 51 INFO @ Sat, 11 Dec 2021 15:45:07: #1 total tags in treatment: 13706244 INFO @ Sat, 11 Dec 2021 15:45:07: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:45:07: #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 15:45:07: #1 tags after filtering in treatment: 13706244 INFO @ Sat, 11 Dec 2021 15:45:07: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 15:45:07: #1 finished! INFO @ Sat, 11 Dec 2021 15:45:07: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:45:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:45:08: #2 number of paired peaks: 146 WARNING @ Sat, 11 Dec 2021 15:45:08: Fewer paired peaks (146) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 146 pairs to build model! INFO @ Sat, 11 Dec 2021 15:45:08: start model_add_line... INFO @ Sat, 11 Dec 2021 15:45:08: start X-correlation... INFO @ Sat, 11 Dec 2021 15:45:08: end of X-cor INFO @ Sat, 11 Dec 2021 15:45:08: #2 finished! INFO @ Sat, 11 Dec 2021 15:45:08: #2 predicted fragment length is 75 bps INFO @ Sat, 11 Dec 2021 15:45:08: #2 alternative fragment length(s) may be 75 bps INFO @ Sat, 11 Dec 2021 15:45:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7434134/SRX7434134.05_model.r WARNING @ Sat, 11 Dec 2021 15:45:08: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 15:45:08: #2 You may need to consider one of the other alternative d(s): 75 WARNING @ Sat, 11 Dec 2021 15:45:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 15:45:08: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:45:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:45:09: 12000000 INFO @ Sat, 11 Dec 2021 15:45:10: 7000000 INFO @ Sat, 11 Dec 2021 15:45:14: 13000000 INFO @ Sat, 11 Dec 2021 15:45:15: 8000000 INFO @ Sat, 11 Dec 2021 15:45:18: #1 tag size is determined as 51 bps INFO @ Sat, 11 Dec 2021 15:45:18: #1 tag size = 51 INFO @ Sat, 11 Dec 2021 15:45:18: #1 total tags in treatment: 13706244 INFO @ Sat, 11 Dec 2021 15:45:18: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:45:18: #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 15:45:19: #1 tags after filtering in treatment: 13706244 INFO @ Sat, 11 Dec 2021 15:45:19: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 15:45:19: #1 finished! INFO @ Sat, 11 Dec 2021 15:45:19: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:45:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:45:19: #2 number of paired peaks: 146 WARNING @ Sat, 11 Dec 2021 15:45:19: Fewer paired peaks (146) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 146 pairs to build model! INFO @ Sat, 11 Dec 2021 15:45:19: start model_add_line... INFO @ Sat, 11 Dec 2021 15:45:20: start X-correlation... INFO @ Sat, 11 Dec 2021 15:45:20: end of X-cor INFO @ Sat, 11 Dec 2021 15:45:20: #2 finished! INFO @ Sat, 11 Dec 2021 15:45:20: #2 predicted fragment length is 75 bps INFO @ Sat, 11 Dec 2021 15:45:20: #2 alternative fragment length(s) may be 75 bps INFO @ Sat, 11 Dec 2021 15:45:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7434134/SRX7434134.10_model.r WARNING @ Sat, 11 Dec 2021 15:45:20: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 15:45:20: #2 You may need to consider one of the other alternative d(s): 75 WARNING @ Sat, 11 Dec 2021 15:45:20: #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 15:45:20: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:45:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:45:21: 9000000 INFO @ Sat, 11 Dec 2021 15:45:26: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 15:45:31: 11000000 INFO @ Sat, 11 Dec 2021 15:45:34: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:45:36: 12000000 INFO @ Sat, 11 Dec 2021 15:45:42: 13000000 INFO @ Sat, 11 Dec 2021 15:45:45: #1 tag size is determined as 51 bps INFO @ Sat, 11 Dec 2021 15:45:45: #1 tag size = 51 INFO @ Sat, 11 Dec 2021 15:45:45: #1 total tags in treatment: 13706244 INFO @ Sat, 11 Dec 2021 15:45:45: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:45:45: #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 15:45:45: #1 tags after filtering in treatment: 13706244 INFO @ Sat, 11 Dec 2021 15:45:45: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 15:45:45: #1 finished! INFO @ Sat, 11 Dec 2021 15:45:45: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:45:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:45:46: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:45:46: #2 number of paired peaks: 146 WARNING @ Sat, 11 Dec 2021 15:45:46: Fewer paired peaks (146) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 146 pairs to build model! INFO @ Sat, 11 Dec 2021 15:45:46: start model_add_line... INFO @ Sat, 11 Dec 2021 15:45:46: start X-correlation... INFO @ Sat, 11 Dec 2021 15:45:46: end of X-cor INFO @ Sat, 11 Dec 2021 15:45:46: #2 finished! INFO @ Sat, 11 Dec 2021 15:45:46: #2 predicted fragment length is 75 bps INFO @ Sat, 11 Dec 2021 15:45:46: #2 alternative fragment length(s) may be 75 bps INFO @ Sat, 11 Dec 2021 15:45:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7434134/SRX7434134.20_model.r WARNING @ Sat, 11 Dec 2021 15:45:46: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 15:45:46: #2 You may need to consider one of the other alternative d(s): 75 WARNING @ Sat, 11 Dec 2021 15:45:46: #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 15:45:46: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:45:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:45:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7434134/SRX7434134.05_peaks.xls INFO @ Sat, 11 Dec 2021 15:45:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7434134/SRX7434134.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:45:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7434134/SRX7434134.05_summits.bed INFO @ Sat, 11 Dec 2021 15:45:48: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1801 records, 4 fields): 4 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 15:45:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7434134/SRX7434134.10_peaks.xls INFO @ Sat, 11 Dec 2021 15:45:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7434134/SRX7434134.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:46:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7434134/SRX7434134.10_summits.bed INFO @ Sat, 11 Dec 2021 15:46:00: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (955 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 15:46:13: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:46:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7434134/SRX7434134.20_peaks.xls INFO @ Sat, 11 Dec 2021 15:46:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7434134/SRX7434134.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:46:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7434134/SRX7434134.20_summits.bed INFO @ Sat, 11 Dec 2021 15:46:26: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (552 records, 4 fields): 1 millis CompletedMACS2peakCalling