Job ID = 14172333 SRX = SRX7434116 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 20305682 spots for SRR10759882/SRR10759882.sra Written 20305682 spots for SRR10759882/SRR10759882.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172812 ("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: 00:06:50 20305682 reads; of these: 20305682 (100.00%) were unpaired; of these: 2162366 (10.65%) aligned 0 times 13060309 (64.32%) aligned exactly 1 time 5083007 (25.03%) aligned >1 times 89.35% overall alignment rate Time searching: 00:06:50 Overall time: 00:06:50 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] 2227184 / 18143316 = 0.1228 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 15:22:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7434116/SRX7434116.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7434116/SRX7434116.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7434116/SRX7434116.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7434116/SRX7434116.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 15:22:23: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:22:23: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:22:29: 1000000 INFO @ Sat, 11 Dec 2021 15:22:34: 2000000 INFO @ Sat, 11 Dec 2021 15:22:39: 3000000 INFO @ Sat, 11 Dec 2021 15:22:44: 4000000 INFO @ Sat, 11 Dec 2021 15:22:50: 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 15:22:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7434116/SRX7434116.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7434116/SRX7434116.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7434116/SRX7434116.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7434116/SRX7434116.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 15:22:53: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:22:53: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:22:55: 6000000 INFO @ Sat, 11 Dec 2021 15:22:59: 1000000 INFO @ Sat, 11 Dec 2021 15:23:01: 7000000 INFO @ Sat, 11 Dec 2021 15:23:05: 2000000 INFO @ Sat, 11 Dec 2021 15:23:07: 8000000 INFO @ Sat, 11 Dec 2021 15:23:11: 3000000 INFO @ Sat, 11 Dec 2021 15:23:12: 9000000 INFO @ Sat, 11 Dec 2021 15:23:16: 4000000 INFO @ Sat, 11 Dec 2021 15:23:18: 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 15:23:22: 5000000 INFO @ Sat, 11 Dec 2021 15:23:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7434116/SRX7434116.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7434116/SRX7434116.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7434116/SRX7434116.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7434116/SRX7434116.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 15:23:23: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:23:23: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:23:24: 11000000 INFO @ Sat, 11 Dec 2021 15:23:28: 6000000 INFO @ Sat, 11 Dec 2021 15:23:30: 1000000 INFO @ Sat, 11 Dec 2021 15:23:30: 12000000 INFO @ Sat, 11 Dec 2021 15:23:35: 7000000 INFO @ Sat, 11 Dec 2021 15:23:36: 2000000 INFO @ Sat, 11 Dec 2021 15:23:37: 13000000 INFO @ Sat, 11 Dec 2021 15:23:41: 8000000 INFO @ Sat, 11 Dec 2021 15:23:42: 3000000 INFO @ Sat, 11 Dec 2021 15:23:43: 14000000 INFO @ Sat, 11 Dec 2021 15:23:47: 9000000 INFO @ Sat, 11 Dec 2021 15:23:48: 4000000 INFO @ Sat, 11 Dec 2021 15:23:48: 15000000 INFO @ Sat, 11 Dec 2021 15:23:53: 10000000 INFO @ Sat, 11 Dec 2021 15:23:54: 5000000 INFO @ Sat, 11 Dec 2021 15:23:54: #1 tag size is determined as 51 bps INFO @ Sat, 11 Dec 2021 15:23:54: #1 tag size = 51 INFO @ Sat, 11 Dec 2021 15:23:54: #1 total tags in treatment: 15916132 INFO @ Sat, 11 Dec 2021 15:23:54: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:23:54: #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 15:23:55: #1 tags after filtering in treatment: 15916132 INFO @ Sat, 11 Dec 2021 15:23:55: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 15:23:55: #1 finished! INFO @ Sat, 11 Dec 2021 15:23:55: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:23:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:23:56: #2 number of paired peaks: 110 WARNING @ Sat, 11 Dec 2021 15:23:56: Fewer paired peaks (110) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 110 pairs to build model! INFO @ Sat, 11 Dec 2021 15:23:56: start model_add_line... INFO @ Sat, 11 Dec 2021 15:23:56: start X-correlation... INFO @ Sat, 11 Dec 2021 15:23:56: end of X-cor INFO @ Sat, 11 Dec 2021 15:23:56: #2 finished! INFO @ Sat, 11 Dec 2021 15:23:56: #2 predicted fragment length is 67 bps INFO @ Sat, 11 Dec 2021 15:23:56: #2 alternative fragment length(s) may be 67,89 bps INFO @ Sat, 11 Dec 2021 15:23:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7434116/SRX7434116.05_model.r WARNING @ Sat, 11 Dec 2021 15:23:56: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 15:23:56: #2 You may need to consider one of the other alternative d(s): 67,89 WARNING @ Sat, 11 Dec 2021 15:23:56: #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 15:23:56: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:23:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:23:58: 11000000 INFO @ Sat, 11 Dec 2021 15:24:00: 6000000 INFO @ Sat, 11 Dec 2021 15:24:04: 12000000 INFO @ Sat, 11 Dec 2021 15:24:06: 7000000 INFO @ Sat, 11 Dec 2021 15:24:10: 13000000 INFO @ Sat, 11 Dec 2021 15:24:11: 8000000 INFO @ Sat, 11 Dec 2021 15:24:16: 14000000 INFO @ Sat, 11 Dec 2021 15:24:17: 9000000 INFO @ Sat, 11 Dec 2021 15:24:21: 15000000 INFO @ Sat, 11 Dec 2021 15:24:22: 10000000 INFO @ Sat, 11 Dec 2021 15:24:24: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:24:27: #1 tag size is determined as 51 bps INFO @ Sat, 11 Dec 2021 15:24:27: #1 tag size = 51 INFO @ Sat, 11 Dec 2021 15:24:27: #1 total tags in treatment: 15916132 INFO @ Sat, 11 Dec 2021 15:24:27: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:24:27: #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 15:24:27: #1 tags after filtering in treatment: 15916132 INFO @ Sat, 11 Dec 2021 15:24:27: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 15:24:27: #1 finished! INFO @ Sat, 11 Dec 2021 15:24:27: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:24:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:24:28: 11000000 INFO @ Sat, 11 Dec 2021 15:24:28: #2 number of paired peaks: 110 WARNING @ Sat, 11 Dec 2021 15:24:28: Fewer paired peaks (110) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 110 pairs to build model! INFO @ Sat, 11 Dec 2021 15:24:28: start model_add_line... INFO @ Sat, 11 Dec 2021 15:24:28: start X-correlation... INFO @ Sat, 11 Dec 2021 15:24:28: end of X-cor INFO @ Sat, 11 Dec 2021 15:24:28: #2 finished! INFO @ Sat, 11 Dec 2021 15:24:28: #2 predicted fragment length is 67 bps INFO @ Sat, 11 Dec 2021 15:24:28: #2 alternative fragment length(s) may be 67,89 bps INFO @ Sat, 11 Dec 2021 15:24:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7434116/SRX7434116.10_model.r WARNING @ Sat, 11 Dec 2021 15:24:28: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 15:24:28: #2 You may need to consider one of the other alternative d(s): 67,89 WARNING @ Sat, 11 Dec 2021 15:24:28: #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 15:24:28: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:24:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:24:33: 12000000 INFO @ Sat, 11 Dec 2021 15:24:39: 13000000 INFO @ Sat, 11 Dec 2021 15:24:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7434116/SRX7434116.05_peaks.xls INFO @ Sat, 11 Dec 2021 15:24:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7434116/SRX7434116.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:24:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7434116/SRX7434116.05_summits.bed INFO @ Sat, 11 Dec 2021 15:24:41: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1782 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 15:24:44: 14000000 INFO @ Sat, 11 Dec 2021 15:24:49: 15000000 INFO @ Sat, 11 Dec 2021 15:24:54: #1 tag size is determined as 51 bps INFO @ Sat, 11 Dec 2021 15:24:54: #1 tag size = 51 INFO @ Sat, 11 Dec 2021 15:24:54: #1 total tags in treatment: 15916132 INFO @ Sat, 11 Dec 2021 15:24:54: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:24:54: #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 15:24:54: #1 tags after filtering in treatment: 15916132 INFO @ Sat, 11 Dec 2021 15:24:54: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 15:24:54: #1 finished! INFO @ Sat, 11 Dec 2021 15:24:54: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:24:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:24:56: #2 number of paired peaks: 110 WARNING @ Sat, 11 Dec 2021 15:24:56: Fewer paired peaks (110) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 110 pairs to build model! INFO @ Sat, 11 Dec 2021 15:24:56: start model_add_line... INFO @ Sat, 11 Dec 2021 15:24:56: start X-correlation... INFO @ Sat, 11 Dec 2021 15:24:56: end of X-cor INFO @ Sat, 11 Dec 2021 15:24:56: #2 finished! INFO @ Sat, 11 Dec 2021 15:24:56: #2 predicted fragment length is 67 bps INFO @ Sat, 11 Dec 2021 15:24:56: #2 alternative fragment length(s) may be 67,89 bps INFO @ Sat, 11 Dec 2021 15:24:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7434116/SRX7434116.20_model.r WARNING @ Sat, 11 Dec 2021 15:24:56: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 15:24:56: #2 You may need to consider one of the other alternative d(s): 67,89 WARNING @ Sat, 11 Dec 2021 15:24:56: #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 15:24:56: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:24:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:24:56: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 15:25:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7434116/SRX7434116.10_peaks.xls INFO @ Sat, 11 Dec 2021 15:25:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7434116/SRX7434116.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:25:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7434116/SRX7434116.10_summits.bed INFO @ Sat, 11 Dec 2021 15:25:12: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (957 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 15:25:23: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:25:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7434116/SRX7434116.20_peaks.xls INFO @ Sat, 11 Dec 2021 15:25:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7434116/SRX7434116.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:25:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7434116/SRX7434116.20_summits.bed INFO @ Sat, 11 Dec 2021 15:25:39: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (485 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。