Job ID = 14167434 SRX = SRX8688945 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 22781079 spots for SRR12174176/SRR12174176.sra Written 22781079 spots for SRR12174176/SRR12174176.sra fastq に変換しました。 bowtie でマッピング中... Your job 14168068 ("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: 00:06:38 22781079 reads; of these: 22781079 (100.00%) were unpaired; of these: 4564969 (20.04%) aligned 0 times 13762149 (60.41%) aligned exactly 1 time 4453961 (19.55%) aligned >1 times 79.96% overall alignment rate Time searching: 00:06:38 Overall time: 00:06:38 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] 1768886 / 18216110 = 0.0971 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 @ Fri, 10 Dec 2021 12:30:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688945/SRX8688945.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688945/SRX8688945.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688945/SRX8688945.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688945/SRX8688945.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 @ Fri, 10 Dec 2021 12:30:56: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:30:56: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:31:00: 1000000 INFO @ Fri, 10 Dec 2021 12:31:05: 2000000 INFO @ Fri, 10 Dec 2021 12:31:10: 3000000 INFO @ Fri, 10 Dec 2021 12:31:14: 4000000 INFO @ Fri, 10 Dec 2021 12:31:19: 5000000 INFO @ Fri, 10 Dec 2021 12:31:23: 6000000 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 @ Fri, 10 Dec 2021 12:31:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688945/SRX8688945.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688945/SRX8688945.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688945/SRX8688945.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688945/SRX8688945.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 @ Fri, 10 Dec 2021 12:31:25: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:31:25: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:31:28: 7000000 INFO @ Fri, 10 Dec 2021 12:31:30: 1000000 INFO @ Fri, 10 Dec 2021 12:31:33: 8000000 INFO @ Fri, 10 Dec 2021 12:31:35: 2000000 INFO @ Fri, 10 Dec 2021 12:31:38: 9000000 INFO @ Fri, 10 Dec 2021 12:31:40: 3000000 INFO @ Fri, 10 Dec 2021 12:31:42: 10000000 INFO @ Fri, 10 Dec 2021 12:31:45: 4000000 INFO @ Fri, 10 Dec 2021 12:31:47: 11000000 INFO @ Fri, 10 Dec 2021 12:31:50: 5000000 INFO @ Fri, 10 Dec 2021 12:31:52: 12000000 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 @ Fri, 10 Dec 2021 12:31:54: 6000000 INFO @ Fri, 10 Dec 2021 12:31:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688945/SRX8688945.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688945/SRX8688945.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688945/SRX8688945.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688945/SRX8688945.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 @ Fri, 10 Dec 2021 12:31:55: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:31:55: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:31:57: 13000000 INFO @ Fri, 10 Dec 2021 12:31:59: 7000000 INFO @ Fri, 10 Dec 2021 12:32:01: 1000000 INFO @ Fri, 10 Dec 2021 12:32:02: 14000000 INFO @ Fri, 10 Dec 2021 12:32:04: 8000000 INFO @ Fri, 10 Dec 2021 12:32:07: 15000000 INFO @ Fri, 10 Dec 2021 12:32:07: 2000000 INFO @ Fri, 10 Dec 2021 12:32:09: 9000000 INFO @ Fri, 10 Dec 2021 12:32:11: 16000000 INFO @ Fri, 10 Dec 2021 12:32:13: 3000000 INFO @ Fri, 10 Dec 2021 12:32:14: 10000000 INFO @ Fri, 10 Dec 2021 12:32:14: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 12:32:14: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 12:32:14: #1 total tags in treatment: 16447224 INFO @ Fri, 10 Dec 2021 12:32:14: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:32:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 12:32:14: #1 tags after filtering in treatment: 16447224 INFO @ Fri, 10 Dec 2021 12:32:14: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:32:14: #1 finished! INFO @ Fri, 10 Dec 2021 12:32:14: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:32:14: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:32:15: #2 number of paired peaks: 190 WARNING @ Fri, 10 Dec 2021 12:32:15: Fewer paired peaks (190) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 190 pairs to build model! INFO @ Fri, 10 Dec 2021 12:32:15: start model_add_line... INFO @ Fri, 10 Dec 2021 12:32:15: start X-correlation... INFO @ Fri, 10 Dec 2021 12:32:15: end of X-cor INFO @ Fri, 10 Dec 2021 12:32:15: #2 finished! INFO @ Fri, 10 Dec 2021 12:32:15: #2 predicted fragment length is 43 bps INFO @ Fri, 10 Dec 2021 12:32:15: #2 alternative fragment length(s) may be 43 bps INFO @ Fri, 10 Dec 2021 12:32:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688945/SRX8688945.05_model.r WARNING @ Fri, 10 Dec 2021 12:32:15: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 12:32:15: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Fri, 10 Dec 2021 12:32:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 12:32:15: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:32:15: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:32:18: 4000000 INFO @ Fri, 10 Dec 2021 12:32:19: 11000000 INFO @ Fri, 10 Dec 2021 12:32:23: 12000000 INFO @ Fri, 10 Dec 2021 12:32:24: 5000000 INFO @ Fri, 10 Dec 2021 12:32:28: 13000000 INFO @ Fri, 10 Dec 2021 12:32:29: 6000000 INFO @ Fri, 10 Dec 2021 12:32:33: 14000000 INFO @ Fri, 10 Dec 2021 12:32:35: 7000000 INFO @ Fri, 10 Dec 2021 12:32:38: 15000000 INFO @ Fri, 10 Dec 2021 12:32:40: 8000000 INFO @ Fri, 10 Dec 2021 12:32:43: 16000000 INFO @ Fri, 10 Dec 2021 12:32:44: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:32:45: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 12:32:45: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 12:32:45: #1 total tags in treatment: 16447224 INFO @ Fri, 10 Dec 2021 12:32:45: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:32:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 12:32:45: #1 tags after filtering in treatment: 16447224 INFO @ Fri, 10 Dec 2021 12:32:45: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:32:45: #1 finished! INFO @ Fri, 10 Dec 2021 12:32:45: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:32:45: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:32:46: 9000000 INFO @ Fri, 10 Dec 2021 12:32:46: #2 number of paired peaks: 190 WARNING @ Fri, 10 Dec 2021 12:32:46: Fewer paired peaks (190) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 190 pairs to build model! INFO @ Fri, 10 Dec 2021 12:32:46: start model_add_line... INFO @ Fri, 10 Dec 2021 12:32:46: start X-correlation... INFO @ Fri, 10 Dec 2021 12:32:46: end of X-cor INFO @ Fri, 10 Dec 2021 12:32:46: #2 finished! INFO @ Fri, 10 Dec 2021 12:32:46: #2 predicted fragment length is 43 bps INFO @ Fri, 10 Dec 2021 12:32:46: #2 alternative fragment length(s) may be 43 bps INFO @ Fri, 10 Dec 2021 12:32:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688945/SRX8688945.10_model.r WARNING @ Fri, 10 Dec 2021 12:32:46: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 12:32:46: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Fri, 10 Dec 2021 12:32:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 12:32:46: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:32:46: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:32:51: 10000000 INFO @ Fri, 10 Dec 2021 12:32:56: 11000000 INFO @ Fri, 10 Dec 2021 12:32:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688945/SRX8688945.05_peaks.xls INFO @ Fri, 10 Dec 2021 12:32:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688945/SRX8688945.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:32:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688945/SRX8688945.05_summits.bed INFO @ Fri, 10 Dec 2021 12:32:58: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1607 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 12:33:02: 12000000 INFO @ Fri, 10 Dec 2021 12:33:07: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 12:33:13: 14000000 INFO @ Fri, 10 Dec 2021 12:33:16: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:33:18: 15000000 INFO @ Fri, 10 Dec 2021 12:33:24: 16000000 INFO @ Fri, 10 Dec 2021 12:33:27: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 12:33:27: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 12:33:27: #1 total tags in treatment: 16447224 INFO @ Fri, 10 Dec 2021 12:33:27: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:33:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 12:33:27: #1 tags after filtering in treatment: 16447224 INFO @ Fri, 10 Dec 2021 12:33:27: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:33:27: #1 finished! INFO @ Fri, 10 Dec 2021 12:33:27: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:33:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:33:28: #2 number of paired peaks: 190 WARNING @ Fri, 10 Dec 2021 12:33:28: Fewer paired peaks (190) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 190 pairs to build model! INFO @ Fri, 10 Dec 2021 12:33:28: start model_add_line... INFO @ Fri, 10 Dec 2021 12:33:28: start X-correlation... INFO @ Fri, 10 Dec 2021 12:33:28: end of X-cor INFO @ Fri, 10 Dec 2021 12:33:28: #2 finished! INFO @ Fri, 10 Dec 2021 12:33:28: #2 predicted fragment length is 43 bps INFO @ Fri, 10 Dec 2021 12:33:28: #2 alternative fragment length(s) may be 43 bps INFO @ Fri, 10 Dec 2021 12:33:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688945/SRX8688945.20_model.r WARNING @ Fri, 10 Dec 2021 12:33:28: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 12:33:28: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Fri, 10 Dec 2021 12:33:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 12:33:28: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:33:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:33:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688945/SRX8688945.10_peaks.xls INFO @ Fri, 10 Dec 2021 12:33:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688945/SRX8688945.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:33:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688945/SRX8688945.10_summits.bed INFO @ Fri, 10 Dec 2021 12:33:30: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1378 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 12:33:57: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:34:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688945/SRX8688945.20_peaks.xls INFO @ Fri, 10 Dec 2021 12:34:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688945/SRX8688945.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:34:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688945/SRX8688945.20_summits.bed INFO @ Fri, 10 Dec 2021 12:34:11: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (1094 records, 4 fields): 3 millis CompletedMACS2peakCalling