Job ID = 16438016 SRX = SRX14148454 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 20600850 spots for SRR17992816/SRR17992816.sra Written 20600850 spots for SRR17992816/SRR17992816.sra fastq に変換しました。 bowtie でマッピング中... Your job 16438070 ("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: 00:09:34 20600850 reads; of these: 20600850 (100.00%) were unpaired; of these: 1073160 (5.21%) aligned 0 times 13610491 (66.07%) aligned exactly 1 time 5917199 (28.72%) aligned >1 times 94.79% overall alignment rate Time searching: 00:09:34 Overall time: 00:09:34 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] 2550462 / 19527690 = 0.1306 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 13:30:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14148454/SRX14148454.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14148454/SRX14148454.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14148454/SRX14148454.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14148454/SRX14148454.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 @ Tue, 02 Aug 2022 13:30:00: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:30:00: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:30:08: 1000000 INFO @ Tue, 02 Aug 2022 13:30:14: 2000000 INFO @ Tue, 02 Aug 2022 13:30:20: 3000000 INFO @ Tue, 02 Aug 2022 13:30:26: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 13:30:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14148454/SRX14148454.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14148454/SRX14148454.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14148454/SRX14148454.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14148454/SRX14148454.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 @ Tue, 02 Aug 2022 13:30:29: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:30:29: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:30:33: 5000000 INFO @ Tue, 02 Aug 2022 13:30:36: 1000000 INFO @ Tue, 02 Aug 2022 13:30:40: 6000000 INFO @ Tue, 02 Aug 2022 13:30:43: 2000000 INFO @ Tue, 02 Aug 2022 13:30:46: 7000000 INFO @ Tue, 02 Aug 2022 13:30:50: 3000000 INFO @ Tue, 02 Aug 2022 13:30:53: 8000000 INFO @ Tue, 02 Aug 2022 13:30:57: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 13:30:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14148454/SRX14148454.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14148454/SRX14148454.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14148454/SRX14148454.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14148454/SRX14148454.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 @ Tue, 02 Aug 2022 13:30:59: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:30:59: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:31:00: 9000000 INFO @ Tue, 02 Aug 2022 13:31:04: 5000000 INFO @ Tue, 02 Aug 2022 13:31:07: 1000000 INFO @ Tue, 02 Aug 2022 13:31:08: 10000000 INFO @ Tue, 02 Aug 2022 13:31:12: 6000000 INFO @ Tue, 02 Aug 2022 13:31:14: 2000000 INFO @ Tue, 02 Aug 2022 13:31:15: 11000000 INFO @ Tue, 02 Aug 2022 13:31:19: 7000000 INFO @ Tue, 02 Aug 2022 13:31:22: 3000000 INFO @ Tue, 02 Aug 2022 13:31:23: 12000000 INFO @ Tue, 02 Aug 2022 13:31:26: 8000000 INFO @ Tue, 02 Aug 2022 13:31:29: 4000000 INFO @ Tue, 02 Aug 2022 13:31:30: 13000000 INFO @ Tue, 02 Aug 2022 13:31:34: 9000000 INFO @ Tue, 02 Aug 2022 13:31:36: 5000000 INFO @ Tue, 02 Aug 2022 13:31:37: 14000000 INFO @ Tue, 02 Aug 2022 13:31:41: 10000000 INFO @ Tue, 02 Aug 2022 13:31:44: 6000000 INFO @ Tue, 02 Aug 2022 13:31:45: 15000000 INFO @ Tue, 02 Aug 2022 13:31:48: 11000000 INFO @ Tue, 02 Aug 2022 13:31:51: 7000000 INFO @ Tue, 02 Aug 2022 13:31:52: 16000000 INFO @ Tue, 02 Aug 2022 13:31:55: 12000000 INFO @ Tue, 02 Aug 2022 13:31:58: 8000000 INFO @ Tue, 02 Aug 2022 13:31:59: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 13:31:59: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 13:31:59: #1 total tags in treatment: 16977228 INFO @ Tue, 02 Aug 2022 13:31:59: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:31:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 13:32:00: #1 tags after filtering in treatment: 16977228 INFO @ Tue, 02 Aug 2022 13:32:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:32:00: #1 finished! INFO @ Tue, 02 Aug 2022 13:32:00: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:32:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:32:01: #2 number of paired peaks: 622 WARNING @ Tue, 02 Aug 2022 13:32:01: Fewer paired peaks (622) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 622 pairs to build model! INFO @ Tue, 02 Aug 2022 13:32:01: start model_add_line... INFO @ Tue, 02 Aug 2022 13:32:01: start X-correlation... INFO @ Tue, 02 Aug 2022 13:32:01: end of X-cor INFO @ Tue, 02 Aug 2022 13:32:01: #2 finished! INFO @ Tue, 02 Aug 2022 13:32:01: #2 predicted fragment length is 76 bps INFO @ Tue, 02 Aug 2022 13:32:01: #2 alternative fragment length(s) may be 3,76,579,598 bps INFO @ Tue, 02 Aug 2022 13:32:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14148454/SRX14148454.05_model.r WARNING @ Tue, 02 Aug 2022 13:32:01: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:32:01: #2 You may need to consider one of the other alternative d(s): 3,76,579,598 WARNING @ Tue, 02 Aug 2022 13:32:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 13:32:01: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:32:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:32:02: 13000000 INFO @ Tue, 02 Aug 2022 13:32:05: 9000000 INFO @ Tue, 02 Aug 2022 13:32:10: 14000000 INFO @ Tue, 02 Aug 2022 13:32:12: 10000000 INFO @ Tue, 02 Aug 2022 13:32:17: 15000000 INFO @ Tue, 02 Aug 2022 13:32:19: 11000000 INFO @ Tue, 02 Aug 2022 13:32:24: 16000000 INFO @ Tue, 02 Aug 2022 13:32:26: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 13:32:31: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 13:32:31: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 13:32:31: #1 total tags in treatment: 16977228 INFO @ Tue, 02 Aug 2022 13:32:31: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:32:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 13:32:32: #1 tags after filtering in treatment: 16977228 INFO @ Tue, 02 Aug 2022 13:32:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:32:32: #1 finished! INFO @ Tue, 02 Aug 2022 13:32:32: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:32:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:32:33: #2 number of paired peaks: 622 WARNING @ Tue, 02 Aug 2022 13:32:33: Fewer paired peaks (622) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 622 pairs to build model! INFO @ Tue, 02 Aug 2022 13:32:33: start model_add_line... INFO @ Tue, 02 Aug 2022 13:32:33: start X-correlation... INFO @ Tue, 02 Aug 2022 13:32:33: end of X-cor INFO @ Tue, 02 Aug 2022 13:32:33: #2 finished! INFO @ Tue, 02 Aug 2022 13:32:33: #2 predicted fragment length is 76 bps INFO @ Tue, 02 Aug 2022 13:32:33: #2 alternative fragment length(s) may be 3,76,579,598 bps INFO @ Tue, 02 Aug 2022 13:32:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14148454/SRX14148454.10_model.r WARNING @ Tue, 02 Aug 2022 13:32:33: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:32:33: #2 You may need to consider one of the other alternative d(s): 3,76,579,598 WARNING @ Tue, 02 Aug 2022 13:32:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 13:32:33: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:32:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:32:33: 13000000 INFO @ Tue, 02 Aug 2022 13:32:34: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:32:39: 14000000 INFO @ Tue, 02 Aug 2022 13:32:45: 15000000 INFO @ Tue, 02 Aug 2022 13:32:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14148454/SRX14148454.05_peaks.xls INFO @ Tue, 02 Aug 2022 13:32:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14148454/SRX14148454.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:32:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14148454/SRX14148454.05_summits.bed INFO @ Tue, 02 Aug 2022 13:32:52: Done! INFO @ Tue, 02 Aug 2022 13:32:52: 16000000 pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3327 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:32:58: #1 tag size is determined as 76 bps INFO @ Tue, 02 Aug 2022 13:32:58: #1 tag size = 76 INFO @ Tue, 02 Aug 2022 13:32:58: #1 total tags in treatment: 16977228 INFO @ Tue, 02 Aug 2022 13:32:58: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:32:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 13:32:58: #1 tags after filtering in treatment: 16977228 INFO @ Tue, 02 Aug 2022 13:32:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:32:58: #1 finished! INFO @ Tue, 02 Aug 2022 13:32:58: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:32:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:32:59: #2 number of paired peaks: 622 WARNING @ Tue, 02 Aug 2022 13:32:59: Fewer paired peaks (622) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 622 pairs to build model! INFO @ Tue, 02 Aug 2022 13:32:59: start model_add_line... INFO @ Tue, 02 Aug 2022 13:32:59: start X-correlation... INFO @ Tue, 02 Aug 2022 13:32:59: end of X-cor INFO @ Tue, 02 Aug 2022 13:32:59: #2 finished! INFO @ Tue, 02 Aug 2022 13:32:59: #2 predicted fragment length is 76 bps INFO @ Tue, 02 Aug 2022 13:32:59: #2 alternative fragment length(s) may be 3,76,579,598 bps INFO @ Tue, 02 Aug 2022 13:32:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14148454/SRX14148454.20_model.r WARNING @ Tue, 02 Aug 2022 13:33:00: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:33:00: #2 You may need to consider one of the other alternative d(s): 3,76,579,598 WARNING @ Tue, 02 Aug 2022 13:33:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 13:33:00: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:33:00: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 13:33:06: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:33:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14148454/SRX14148454.10_peaks.xls INFO @ Tue, 02 Aug 2022 13:33:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14148454/SRX14148454.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:33:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14148454/SRX14148454.10_summits.bed INFO @ Tue, 02 Aug 2022 13:33:24: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1874 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:33:34: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:33:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14148454/SRX14148454.20_peaks.xls INFO @ Tue, 02 Aug 2022 13:33:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14148454/SRX14148454.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:33:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14148454/SRX14148454.20_summits.bed INFO @ Tue, 02 Aug 2022 13:33:51: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (974 records, 4 fields): 88 millis CompletedMACS2peakCalling