Job ID = 14167158 SRX = SRX4712963 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 18470763 spots for SRR7874093/SRR7874093.sra Written 18470763 spots for SRR7874093/SRR7874093.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167654 ("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: 00:06:17 18470763 reads; of these: 18470763 (100.00%) were unpaired; of these: 404022 (2.19%) aligned 0 times 13153865 (71.21%) aligned exactly 1 time 4912876 (26.60%) aligned >1 times 97.81% overall alignment rate Time searching: 00:06:17 Overall time: 00:06:17 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] 1737033 / 18066741 = 0.0961 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 10:47:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4712963/SRX4712963.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4712963/SRX4712963.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4712963/SRX4712963.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4712963/SRX4712963.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 10:47:21: #1 read tag files... INFO @ Fri, 10 Dec 2021 10:47:21: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 10:47:28: 1000000 INFO @ Fri, 10 Dec 2021 10:47:37: 2000000 INFO @ Fri, 10 Dec 2021 10:47:44: 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 10:47:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4712963/SRX4712963.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4712963/SRX4712963.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4712963/SRX4712963.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4712963/SRX4712963.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 10:47:49: #1 read tag files... INFO @ Fri, 10 Dec 2021 10:47:49: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 10:47:53: 4000000 INFO @ Fri, 10 Dec 2021 10:47:57: 1000000 INFO @ Fri, 10 Dec 2021 10:48:02: 5000000 INFO @ Fri, 10 Dec 2021 10:48:06: 2000000 INFO @ Fri, 10 Dec 2021 10:48:11: 6000000 INFO @ Fri, 10 Dec 2021 10:48:14: 3000000 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 10:48:20: 7000000 INFO @ Fri, 10 Dec 2021 10:48:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4712963/SRX4712963.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4712963/SRX4712963.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4712963/SRX4712963.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4712963/SRX4712963.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 10:48:20: #1 read tag files... INFO @ Fri, 10 Dec 2021 10:48:20: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 10:48:22: 4000000 INFO @ Fri, 10 Dec 2021 10:48:27: 1000000 INFO @ Fri, 10 Dec 2021 10:48:28: 8000000 INFO @ Fri, 10 Dec 2021 10:48:30: 5000000 INFO @ Fri, 10 Dec 2021 10:48:35: 2000000 INFO @ Fri, 10 Dec 2021 10:48:36: 9000000 INFO @ Fri, 10 Dec 2021 10:48:38: 6000000 INFO @ Fri, 10 Dec 2021 10:48:42: 3000000 INFO @ Fri, 10 Dec 2021 10:48:44: 10000000 INFO @ Fri, 10 Dec 2021 10:48:46: 7000000 INFO @ Fri, 10 Dec 2021 10:48:49: 4000000 INFO @ Fri, 10 Dec 2021 10:48:52: 11000000 INFO @ Fri, 10 Dec 2021 10:48:53: 8000000 INFO @ Fri, 10 Dec 2021 10:48:56: 5000000 INFO @ Fri, 10 Dec 2021 10:49:00: 12000000 INFO @ Fri, 10 Dec 2021 10:49:01: 9000000 INFO @ Fri, 10 Dec 2021 10:49:03: 6000000 INFO @ Fri, 10 Dec 2021 10:49:08: 13000000 INFO @ Fri, 10 Dec 2021 10:49:09: 10000000 INFO @ Fri, 10 Dec 2021 10:49:10: 7000000 INFO @ Fri, 10 Dec 2021 10:49:16: 14000000 INFO @ Fri, 10 Dec 2021 10:49:17: 11000000 INFO @ Fri, 10 Dec 2021 10:49:17: 8000000 INFO @ Fri, 10 Dec 2021 10:49:24: 9000000 INFO @ Fri, 10 Dec 2021 10:49:24: 12000000 INFO @ Fri, 10 Dec 2021 10:49:24: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 10:49:31: 10000000 INFO @ Fri, 10 Dec 2021 10:49:32: 13000000 INFO @ Fri, 10 Dec 2021 10:49:32: 16000000 INFO @ Fri, 10 Dec 2021 10:49:35: #1 tag size is determined as 51 bps INFO @ Fri, 10 Dec 2021 10:49:35: #1 tag size = 51 INFO @ Fri, 10 Dec 2021 10:49:35: #1 total tags in treatment: 16329708 INFO @ Fri, 10 Dec 2021 10:49:35: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 10:49:35: #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 10:49:35: #1 tags after filtering in treatment: 16329708 INFO @ Fri, 10 Dec 2021 10:49:35: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 10:49:35: #1 finished! INFO @ Fri, 10 Dec 2021 10:49:35: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 10:49:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 10:49:36: #2 number of paired peaks: 148 WARNING @ Fri, 10 Dec 2021 10:49:36: Fewer paired peaks (148) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 148 pairs to build model! INFO @ Fri, 10 Dec 2021 10:49:36: start model_add_line... INFO @ Fri, 10 Dec 2021 10:49:36: start X-correlation... INFO @ Fri, 10 Dec 2021 10:49:36: end of X-cor INFO @ Fri, 10 Dec 2021 10:49:36: #2 finished! INFO @ Fri, 10 Dec 2021 10:49:36: #2 predicted fragment length is 46 bps INFO @ Fri, 10 Dec 2021 10:49:36: #2 alternative fragment length(s) may be 46 bps INFO @ Fri, 10 Dec 2021 10:49:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4712963/SRX4712963.05_model.r WARNING @ Fri, 10 Dec 2021 10:49:36: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 10:49:36: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Fri, 10 Dec 2021 10:49:36: #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 10:49:36: #3 Call peaks... INFO @ Fri, 10 Dec 2021 10:49:36: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 10:49:38: 11000000 INFO @ Fri, 10 Dec 2021 10:49:40: 14000000 INFO @ Fri, 10 Dec 2021 10:49:45: 12000000 INFO @ Fri, 10 Dec 2021 10:49:47: 15000000 INFO @ Fri, 10 Dec 2021 10:49:52: 13000000 INFO @ Fri, 10 Dec 2021 10:49:55: 16000000 INFO @ Fri, 10 Dec 2021 10:49:57: #1 tag size is determined as 51 bps INFO @ Fri, 10 Dec 2021 10:49:57: #1 tag size = 51 INFO @ Fri, 10 Dec 2021 10:49:57: #1 total tags in treatment: 16329708 INFO @ Fri, 10 Dec 2021 10:49:57: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 10:49:57: #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 10:49:58: #1 tags after filtering in treatment: 16329708 INFO @ Fri, 10 Dec 2021 10:49:58: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 10:49:58: #1 finished! INFO @ Fri, 10 Dec 2021 10:49:58: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 10:49:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 10:49:59: #2 number of paired peaks: 148 WARNING @ Fri, 10 Dec 2021 10:49:59: Fewer paired peaks (148) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 148 pairs to build model! INFO @ Fri, 10 Dec 2021 10:49:59: start model_add_line... INFO @ Fri, 10 Dec 2021 10:49:59: start X-correlation... INFO @ Fri, 10 Dec 2021 10:49:59: end of X-cor INFO @ Fri, 10 Dec 2021 10:49:59: #2 finished! INFO @ Fri, 10 Dec 2021 10:49:59: #2 predicted fragment length is 46 bps INFO @ Fri, 10 Dec 2021 10:49:59: #2 alternative fragment length(s) may be 46 bps INFO @ Fri, 10 Dec 2021 10:49:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4712963/SRX4712963.10_model.r WARNING @ Fri, 10 Dec 2021 10:49:59: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 10:49:59: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Fri, 10 Dec 2021 10:49:59: #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 10:49:59: #3 Call peaks... INFO @ Fri, 10 Dec 2021 10:49:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 10:49:59: 14000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 10:50:05: 15000000 INFO @ Fri, 10 Dec 2021 10:50:06: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 10:50:11: 16000000 INFO @ Fri, 10 Dec 2021 10:50:13: #1 tag size is determined as 51 bps INFO @ Fri, 10 Dec 2021 10:50:13: #1 tag size = 51 INFO @ Fri, 10 Dec 2021 10:50:13: #1 total tags in treatment: 16329708 INFO @ Fri, 10 Dec 2021 10:50:13: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 10:50:13: #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 10:50:13: #1 tags after filtering in treatment: 16329708 INFO @ Fri, 10 Dec 2021 10:50:13: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 10:50:13: #1 finished! INFO @ Fri, 10 Dec 2021 10:50:13: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 10:50:13: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 10:50:14: #2 number of paired peaks: 148 WARNING @ Fri, 10 Dec 2021 10:50:14: Fewer paired peaks (148) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 148 pairs to build model! INFO @ Fri, 10 Dec 2021 10:50:14: start model_add_line... INFO @ Fri, 10 Dec 2021 10:50:14: start X-correlation... INFO @ Fri, 10 Dec 2021 10:50:14: end of X-cor INFO @ Fri, 10 Dec 2021 10:50:14: #2 finished! INFO @ Fri, 10 Dec 2021 10:50:14: #2 predicted fragment length is 46 bps INFO @ Fri, 10 Dec 2021 10:50:14: #2 alternative fragment length(s) may be 46 bps INFO @ Fri, 10 Dec 2021 10:50:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4712963/SRX4712963.20_model.r WARNING @ Fri, 10 Dec 2021 10:50:14: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 10:50:14: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Fri, 10 Dec 2021 10:50:14: #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 10:50:14: #3 Call peaks... INFO @ Fri, 10 Dec 2021 10:50:14: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 10:50:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4712963/SRX4712963.05_peaks.xls INFO @ Fri, 10 Dec 2021 10:50:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4712963/SRX4712963.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 10:50:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4712963/SRX4712963.05_summits.bed INFO @ Fri, 10 Dec 2021 10:50:21: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2677 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 10:50:29: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 10:50:45: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 10:50:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4712963/SRX4712963.10_peaks.xls INFO @ Fri, 10 Dec 2021 10:50:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4712963/SRX4712963.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 10:50:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4712963/SRX4712963.10_summits.bed INFO @ Fri, 10 Dec 2021 10:50:45: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1517 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 10:50:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4712963/SRX4712963.20_peaks.xls INFO @ Fri, 10 Dec 2021 10:50:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4712963/SRX4712963.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 10:50:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4712963/SRX4712963.20_summits.bed INFO @ Fri, 10 Dec 2021 10:50:59: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (966 records, 4 fields): 3 millis CompletedMACS2peakCalling