Job ID = 14168058 SRX = SRX8688970 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 6248812 spots for SRR12174266/SRR12174266.sra Written 6248812 spots for SRR12174266/SRR12174266.sra fastq に変換しました。 bowtie でマッピング中... Your job 14168765 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:43 6248812 reads; of these: 6248812 (100.00%) were unpaired; of these: 182344 (2.92%) aligned 0 times 4169356 (66.72%) aligned exactly 1 time 1897112 (30.36%) aligned >1 times 97.08% overall alignment rate Time searching: 00:02:44 Overall time: 00:02:44 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_rmdupse_core] 331186 / 6066468 = 0.0546 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 14:57:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688970/SRX8688970.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688970/SRX8688970.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688970/SRX8688970.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688970/SRX8688970.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 14:57:56: #1 read tag files... INFO @ Fri, 10 Dec 2021 14:57:56: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 14:58:03: 1000000 INFO @ Fri, 10 Dec 2021 14:58:11: 2000000 INFO @ Fri, 10 Dec 2021 14:58:18: 3000000 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 14:58:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688970/SRX8688970.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688970/SRX8688970.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688970/SRX8688970.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688970/SRX8688970.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 14:58:25: #1 read tag files... INFO @ Fri, 10 Dec 2021 14:58:25: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 14:58:25: 4000000 INFO @ Fri, 10 Dec 2021 14:58:33: 1000000 INFO @ Fri, 10 Dec 2021 14:58:33: 5000000 INFO @ Fri, 10 Dec 2021 14:58:39: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 14:58:39: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 14:58:39: #1 total tags in treatment: 5735282 INFO @ Fri, 10 Dec 2021 14:58:39: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 14:58:39: #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 14:58:39: #1 tags after filtering in treatment: 5735282 INFO @ Fri, 10 Dec 2021 14:58:39: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 14:58:39: #1 finished! INFO @ Fri, 10 Dec 2021 14:58:39: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 14:58:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 14:58:40: #2 number of paired peaks: 486 WARNING @ Fri, 10 Dec 2021 14:58:40: Fewer paired peaks (486) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 486 pairs to build model! INFO @ Fri, 10 Dec 2021 14:58:40: start model_add_line... INFO @ Fri, 10 Dec 2021 14:58:40: start X-correlation... INFO @ Fri, 10 Dec 2021 14:58:40: end of X-cor INFO @ Fri, 10 Dec 2021 14:58:40: #2 finished! INFO @ Fri, 10 Dec 2021 14:58:40: #2 predicted fragment length is 49 bps INFO @ Fri, 10 Dec 2021 14:58:40: #2 alternative fragment length(s) may be 49 bps INFO @ Fri, 10 Dec 2021 14:58:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688970/SRX8688970.05_model.r WARNING @ Fri, 10 Dec 2021 14:58:40: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 14:58:40: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Fri, 10 Dec 2021 14:58:40: #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 14:58:40: #3 Call peaks... INFO @ Fri, 10 Dec 2021 14:58:40: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 14:58:41: 2000000 INFO @ Fri, 10 Dec 2021 14:58:48: 3000000 INFO @ Fri, 10 Dec 2021 14:58:51: #3 Call peaks for each chromosome... 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 14:58:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688970/SRX8688970.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688970/SRX8688970.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688970/SRX8688970.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688970/SRX8688970.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 14:58:55: #1 read tag files... INFO @ Fri, 10 Dec 2021 14:58:55: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 14:58:56: 4000000 INFO @ Fri, 10 Dec 2021 14:58:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688970/SRX8688970.05_peaks.xls INFO @ Fri, 10 Dec 2021 14:58:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688970/SRX8688970.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 14:58:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688970/SRX8688970.05_summits.bed INFO @ Fri, 10 Dec 2021 14:58:58: Done! pass1 - making usageList (11 chroms): 31 millis pass2 - checking and writing primary data (1422 records, 4 fields): 101 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 14:59:04: 1000000 INFO @ Fri, 10 Dec 2021 14:59:04: 5000000 INFO @ Fri, 10 Dec 2021 14:59:10: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 14:59:10: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 14:59:10: #1 total tags in treatment: 5735282 INFO @ Fri, 10 Dec 2021 14:59:10: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 14:59:10: #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 14:59:10: #1 tags after filtering in treatment: 5735282 INFO @ Fri, 10 Dec 2021 14:59:10: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 14:59:10: #1 finished! INFO @ Fri, 10 Dec 2021 14:59:10: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 14:59:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 14:59:10: #2 number of paired peaks: 486 WARNING @ Fri, 10 Dec 2021 14:59:10: Fewer paired peaks (486) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 486 pairs to build model! INFO @ Fri, 10 Dec 2021 14:59:10: start model_add_line... INFO @ Fri, 10 Dec 2021 14:59:11: start X-correlation... INFO @ Fri, 10 Dec 2021 14:59:11: end of X-cor INFO @ Fri, 10 Dec 2021 14:59:11: #2 finished! INFO @ Fri, 10 Dec 2021 14:59:11: #2 predicted fragment length is 49 bps INFO @ Fri, 10 Dec 2021 14:59:11: #2 alternative fragment length(s) may be 49 bps INFO @ Fri, 10 Dec 2021 14:59:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688970/SRX8688970.10_model.r WARNING @ Fri, 10 Dec 2021 14:59:11: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 14:59:11: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Fri, 10 Dec 2021 14:59:11: #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 14:59:11: #3 Call peaks... INFO @ Fri, 10 Dec 2021 14:59:11: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 14:59:11: 2000000 INFO @ Fri, 10 Dec 2021 14:59:19: 3000000 INFO @ Fri, 10 Dec 2021 14:59:21: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 14:59:26: 4000000 INFO @ Fri, 10 Dec 2021 14:59:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688970/SRX8688970.10_peaks.xls INFO @ Fri, 10 Dec 2021 14:59:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688970/SRX8688970.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 14:59:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688970/SRX8688970.10_summits.bed INFO @ Fri, 10 Dec 2021 14:59:28: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (1208 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 14:59:34: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 14:59:39: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 14:59:39: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 14:59:39: #1 total tags in treatment: 5735282 INFO @ Fri, 10 Dec 2021 14:59:39: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 14:59:39: #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 14:59:39: #1 tags after filtering in treatment: 5735282 INFO @ Fri, 10 Dec 2021 14:59:39: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 14:59:39: #1 finished! INFO @ Fri, 10 Dec 2021 14:59:39: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 14:59:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 14:59:39: #2 number of paired peaks: 486 WARNING @ Fri, 10 Dec 2021 14:59:39: Fewer paired peaks (486) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 486 pairs to build model! INFO @ Fri, 10 Dec 2021 14:59:39: start model_add_line... INFO @ Fri, 10 Dec 2021 14:59:39: start X-correlation... INFO @ Fri, 10 Dec 2021 14:59:39: end of X-cor INFO @ Fri, 10 Dec 2021 14:59:39: #2 finished! INFO @ Fri, 10 Dec 2021 14:59:39: #2 predicted fragment length is 49 bps INFO @ Fri, 10 Dec 2021 14:59:39: #2 alternative fragment length(s) may be 49 bps INFO @ Fri, 10 Dec 2021 14:59:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688970/SRX8688970.20_model.r WARNING @ Fri, 10 Dec 2021 14:59:39: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 14:59:39: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Fri, 10 Dec 2021 14:59:39: #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 14:59:39: #3 Call peaks... INFO @ Fri, 10 Dec 2021 14:59:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 14:59:50: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 14:59:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688970/SRX8688970.20_peaks.xls INFO @ Fri, 10 Dec 2021 14:59:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688970/SRX8688970.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 14:59:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688970/SRX8688970.20_summits.bed INFO @ Fri, 10 Dec 2021 14:59:57: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (907 records, 4 fields): 3 millis CompletedMACS2peakCalling