Job ID = 14170328 SRX = SRX8689104 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 19125540 spots for SRR12174337/SRR12174337.sra Written 19125540 spots for SRR12174337/SRR12174337.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170756 ("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: 00:07:15 19125540 reads; of these: 19125540 (100.00%) were unpaired; of these: 511092 (2.67%) aligned 0 times 13311918 (69.60%) aligned exactly 1 time 5302530 (27.72%) aligned >1 times 97.33% overall alignment rate Time searching: 00:07:15 Overall time: 00:07:15 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] 1621638 / 18614448 = 0.0871 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 06:31:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689104/SRX8689104.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689104/SRX8689104.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689104/SRX8689104.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689104/SRX8689104.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 06:31:23: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:31:23: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:31:29: 1000000 INFO @ Sat, 11 Dec 2021 06:31:34: 2000000 INFO @ Sat, 11 Dec 2021 06:31:40: 3000000 INFO @ Sat, 11 Dec 2021 06:31:45: 4000000 INFO @ Sat, 11 Dec 2021 06:31:51: 5000000 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 06:31:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689104/SRX8689104.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689104/SRX8689104.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689104/SRX8689104.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689104/SRX8689104.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 06:31:53: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:31:53: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:31:56: 6000000 INFO @ Sat, 11 Dec 2021 06:31:59: 1000000 INFO @ Sat, 11 Dec 2021 06:32:02: 7000000 INFO @ Sat, 11 Dec 2021 06:32:05: 2000000 INFO @ Sat, 11 Dec 2021 06:32:07: 8000000 INFO @ Sat, 11 Dec 2021 06:32:10: 3000000 INFO @ Sat, 11 Dec 2021 06:32:13: 9000000 INFO @ Sat, 11 Dec 2021 06:32:16: 4000000 INFO @ Sat, 11 Dec 2021 06:32:18: 10000000 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 06:32:22: 5000000 INFO @ Sat, 11 Dec 2021 06:32:23: 11000000 INFO @ Sat, 11 Dec 2021 06:32:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689104/SRX8689104.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689104/SRX8689104.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689104/SRX8689104.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689104/SRX8689104.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 06:32:23: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:32:23: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:32:27: 6000000 INFO @ Sat, 11 Dec 2021 06:32:28: 12000000 INFO @ Sat, 11 Dec 2021 06:32:29: 1000000 INFO @ Sat, 11 Dec 2021 06:32:33: 7000000 INFO @ Sat, 11 Dec 2021 06:32:34: 13000000 INFO @ Sat, 11 Dec 2021 06:32:35: 2000000 INFO @ Sat, 11 Dec 2021 06:32:38: 8000000 INFO @ Sat, 11 Dec 2021 06:32:39: 14000000 INFO @ Sat, 11 Dec 2021 06:32:40: 3000000 INFO @ Sat, 11 Dec 2021 06:32:44: 9000000 INFO @ Sat, 11 Dec 2021 06:32:45: 15000000 INFO @ Sat, 11 Dec 2021 06:32:46: 4000000 INFO @ Sat, 11 Dec 2021 06:32:49: 10000000 INFO @ Sat, 11 Dec 2021 06:32:50: 16000000 INFO @ Sat, 11 Dec 2021 06:32:52: 5000000 INFO @ Sat, 11 Dec 2021 06:32:54: 11000000 INFO @ Sat, 11 Dec 2021 06:32:56: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:32:56: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:32:56: #1 total tags in treatment: 16992810 INFO @ Sat, 11 Dec 2021 06:32:56: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:32:56: #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 06:32:56: #1 tags after filtering in treatment: 16992810 INFO @ Sat, 11 Dec 2021 06:32:56: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:32:56: #1 finished! INFO @ Sat, 11 Dec 2021 06:32:56: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:32:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:32:57: #2 number of paired peaks: 129 WARNING @ Sat, 11 Dec 2021 06:32:57: Fewer paired peaks (129) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 129 pairs to build model! INFO @ Sat, 11 Dec 2021 06:32:57: start model_add_line... INFO @ Sat, 11 Dec 2021 06:32:57: start X-correlation... INFO @ Sat, 11 Dec 2021 06:32:57: end of X-cor INFO @ Sat, 11 Dec 2021 06:32:57: #2 finished! INFO @ Sat, 11 Dec 2021 06:32:57: #2 predicted fragment length is 45 bps INFO @ Sat, 11 Dec 2021 06:32:57: #2 alternative fragment length(s) may be 45 bps INFO @ Sat, 11 Dec 2021 06:32:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689104/SRX8689104.05_model.r INFO @ Sat, 11 Dec 2021 06:32:57: 6000000 WARNING @ Sat, 11 Dec 2021 06:32:58: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:32:58: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Sat, 11 Dec 2021 06:32:58: #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 06:32:58: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:32:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:32:59: 12000000 INFO @ Sat, 11 Dec 2021 06:33:03: 7000000 INFO @ Sat, 11 Dec 2021 06:33:05: 13000000 INFO @ Sat, 11 Dec 2021 06:33:08: 8000000 INFO @ Sat, 11 Dec 2021 06:33:10: 14000000 INFO @ Sat, 11 Dec 2021 06:33:14: 9000000 INFO @ Sat, 11 Dec 2021 06:33:16: 15000000 INFO @ Sat, 11 Dec 2021 06:33:19: 10000000 INFO @ Sat, 11 Dec 2021 06:33:22: 16000000 INFO @ Sat, 11 Dec 2021 06:33:24: 11000000 INFO @ Sat, 11 Dec 2021 06:33:27: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:33:27: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:33:27: #1 total tags in treatment: 16992810 INFO @ Sat, 11 Dec 2021 06:33:27: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:33:27: #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 06:33:28: #1 tags after filtering in treatment: 16992810 INFO @ Sat, 11 Dec 2021 06:33:28: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:33:28: #1 finished! INFO @ Sat, 11 Dec 2021 06:33:28: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:33:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:33:28: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:33:29: #2 number of paired peaks: 129 WARNING @ Sat, 11 Dec 2021 06:33:29: Fewer paired peaks (129) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 129 pairs to build model! INFO @ Sat, 11 Dec 2021 06:33:29: start model_add_line... INFO @ Sat, 11 Dec 2021 06:33:29: start X-correlation... INFO @ Sat, 11 Dec 2021 06:33:29: end of X-cor INFO @ Sat, 11 Dec 2021 06:33:29: #2 finished! INFO @ Sat, 11 Dec 2021 06:33:29: #2 predicted fragment length is 45 bps INFO @ Sat, 11 Dec 2021 06:33:29: #2 alternative fragment length(s) may be 45 bps INFO @ Sat, 11 Dec 2021 06:33:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689104/SRX8689104.10_model.r WARNING @ Sat, 11 Dec 2021 06:33:29: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:33:29: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Sat, 11 Dec 2021 06:33:29: #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 06:33:29: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:33:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:33:29: 12000000 INFO @ Sat, 11 Dec 2021 06:33:35: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 06:33:40: 14000000 INFO @ Sat, 11 Dec 2021 06:33:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689104/SRX8689104.05_peaks.xls INFO @ Sat, 11 Dec 2021 06:33:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689104/SRX8689104.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:33:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689104/SRX8689104.05_summits.bed INFO @ Sat, 11 Dec 2021 06:33:43: Done! INFO @ Sat, 11 Dec 2021 06:33:46: 15000000 pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (1691 records, 4 fields): 60 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 06:33:51: 16000000 INFO @ Sat, 11 Dec 2021 06:33:56: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:33:56: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:33:56: #1 total tags in treatment: 16992810 INFO @ Sat, 11 Dec 2021 06:33:56: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:33:56: #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 06:33:57: #1 tags after filtering in treatment: 16992810 INFO @ Sat, 11 Dec 2021 06:33:57: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:33:57: #1 finished! INFO @ Sat, 11 Dec 2021 06:33:57: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:33:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:33:58: #2 number of paired peaks: 129 WARNING @ Sat, 11 Dec 2021 06:33:58: Fewer paired peaks (129) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 129 pairs to build model! INFO @ Sat, 11 Dec 2021 06:33:58: start model_add_line... INFO @ Sat, 11 Dec 2021 06:33:58: start X-correlation... INFO @ Sat, 11 Dec 2021 06:33:58: end of X-cor INFO @ Sat, 11 Dec 2021 06:33:58: #2 finished! INFO @ Sat, 11 Dec 2021 06:33:58: #2 predicted fragment length is 45 bps INFO @ Sat, 11 Dec 2021 06:33:58: #2 alternative fragment length(s) may be 45 bps INFO @ Sat, 11 Dec 2021 06:33:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689104/SRX8689104.20_model.r WARNING @ Sat, 11 Dec 2021 06:33:58: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:33:58: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Sat, 11 Dec 2021 06:33:58: #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 06:33:58: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:33:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:33:58: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:34:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689104/SRX8689104.10_peaks.xls INFO @ Sat, 11 Dec 2021 06:34:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689104/SRX8689104.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:34:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689104/SRX8689104.10_summits.bed INFO @ Sat, 11 Dec 2021 06:34:13: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1264 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 06:34:27: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:34:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689104/SRX8689104.20_peaks.xls INFO @ Sat, 11 Dec 2021 06:34:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689104/SRX8689104.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:34:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689104/SRX8689104.20_summits.bed INFO @ Sat, 11 Dec 2021 06:34:42: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (950 records, 4 fields): 3 millis CompletedMACS2peakCalling