Job ID = 14167067 SRX = SRX7723687 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 26497225 spots for SRR11084643/SRR11084643.sra Written 26497225 spots for SRR11084643/SRR11084643.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167506 ("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: 00:21:08 26497225 reads; of these: 26497225 (100.00%) were unpaired; of these: 3394683 (12.81%) aligned 0 times 13060864 (49.29%) aligned exactly 1 time 10041678 (37.90%) aligned >1 times 87.19% overall alignment rate Time searching: 00:21:08 Overall time: 00:21:08 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 12 files... [bam_rmdupse_core] 12651048 / 23102542 = 0.5476 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 09:57:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7723687/SRX7723687.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7723687/SRX7723687.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7723687/SRX7723687.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7723687/SRX7723687.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 09:57:50: #1 read tag files... INFO @ Fri, 10 Dec 2021 09:57:50: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 09:57:57: 1000000 INFO @ Fri, 10 Dec 2021 09:58:04: 2000000 INFO @ Fri, 10 Dec 2021 09:58:11: 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 09:58:18: 4000000 INFO @ Fri, 10 Dec 2021 09:58:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7723687/SRX7723687.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7723687/SRX7723687.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7723687/SRX7723687.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7723687/SRX7723687.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 09:58:19: #1 read tag files... INFO @ Fri, 10 Dec 2021 09:58:19: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 09:58:26: 5000000 INFO @ Fri, 10 Dec 2021 09:58:26: 1000000 INFO @ Fri, 10 Dec 2021 09:58:34: 2000000 INFO @ Fri, 10 Dec 2021 09:58:34: 6000000 INFO @ Fri, 10 Dec 2021 09:58:41: 3000000 INFO @ Fri, 10 Dec 2021 09:58:42: 7000000 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 09:58:48: 4000000 INFO @ Fri, 10 Dec 2021 09:58:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7723687/SRX7723687.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7723687/SRX7723687.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7723687/SRX7723687.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7723687/SRX7723687.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 09:58:49: #1 read tag files... INFO @ Fri, 10 Dec 2021 09:58:49: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 09:58:50: 8000000 INFO @ Fri, 10 Dec 2021 09:58:55: 5000000 INFO @ Fri, 10 Dec 2021 09:58:57: 1000000 INFO @ Fri, 10 Dec 2021 09:58:58: 9000000 INFO @ Fri, 10 Dec 2021 09:59:02: 6000000 INFO @ Fri, 10 Dec 2021 09:59:04: 2000000 INFO @ Fri, 10 Dec 2021 09:59:07: 10000000 INFO @ Fri, 10 Dec 2021 09:59:09: 7000000 INFO @ Fri, 10 Dec 2021 09:59:11: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 09:59:11: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 09:59:11: #1 total tags in treatment: 10451494 INFO @ Fri, 10 Dec 2021 09:59:11: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 09:59:11: #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 09:59:11: #1 tags after filtering in treatment: 10451494 INFO @ Fri, 10 Dec 2021 09:59:11: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 09:59:11: #1 finished! INFO @ Fri, 10 Dec 2021 09:59:11: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 09:59:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 09:59:11: 3000000 INFO @ Fri, 10 Dec 2021 09:59:12: #2 number of paired peaks: 484 WARNING @ Fri, 10 Dec 2021 09:59:12: Fewer paired peaks (484) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 484 pairs to build model! INFO @ Fri, 10 Dec 2021 09:59:12: start model_add_line... INFO @ Fri, 10 Dec 2021 09:59:12: start X-correlation... INFO @ Fri, 10 Dec 2021 09:59:12: end of X-cor INFO @ Fri, 10 Dec 2021 09:59:12: #2 finished! INFO @ Fri, 10 Dec 2021 09:59:12: #2 predicted fragment length is 66 bps INFO @ Fri, 10 Dec 2021 09:59:12: #2 alternative fragment length(s) may be 66 bps INFO @ Fri, 10 Dec 2021 09:59:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723687/SRX7723687.05_model.r WARNING @ Fri, 10 Dec 2021 09:59:12: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 09:59:12: #2 You may need to consider one of the other alternative d(s): 66 WARNING @ Fri, 10 Dec 2021 09:59:12: #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 09:59:12: #3 Call peaks... INFO @ Fri, 10 Dec 2021 09:59:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 09:59:17: 8000000 INFO @ Fri, 10 Dec 2021 09:59:18: 4000000 INFO @ Fri, 10 Dec 2021 09:59:24: 9000000 INFO @ Fri, 10 Dec 2021 09:59:25: 5000000 INFO @ Fri, 10 Dec 2021 09:59:31: 10000000 INFO @ Fri, 10 Dec 2021 09:59:32: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 09:59:32: 6000000 INFO @ Fri, 10 Dec 2021 09:59:34: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 09:59:34: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 09:59:34: #1 total tags in treatment: 10451494 INFO @ Fri, 10 Dec 2021 09:59:34: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 09:59:34: #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 09:59:34: #1 tags after filtering in treatment: 10451494 INFO @ Fri, 10 Dec 2021 09:59:34: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 09:59:34: #1 finished! INFO @ Fri, 10 Dec 2021 09:59:34: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 09:59:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 09:59:35: #2 number of paired peaks: 484 WARNING @ Fri, 10 Dec 2021 09:59:35: Fewer paired peaks (484) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 484 pairs to build model! INFO @ Fri, 10 Dec 2021 09:59:35: start model_add_line... INFO @ Fri, 10 Dec 2021 09:59:35: start X-correlation... INFO @ Fri, 10 Dec 2021 09:59:35: end of X-cor INFO @ Fri, 10 Dec 2021 09:59:35: #2 finished! INFO @ Fri, 10 Dec 2021 09:59:35: #2 predicted fragment length is 66 bps INFO @ Fri, 10 Dec 2021 09:59:35: #2 alternative fragment length(s) may be 66 bps INFO @ Fri, 10 Dec 2021 09:59:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723687/SRX7723687.10_model.r WARNING @ Fri, 10 Dec 2021 09:59:35: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 09:59:35: #2 You may need to consider one of the other alternative d(s): 66 WARNING @ Fri, 10 Dec 2021 09:59:35: #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 09:59:35: #3 Call peaks... INFO @ Fri, 10 Dec 2021 09:59:35: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 09:59:39: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 09:59:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723687/SRX7723687.05_peaks.xls INFO @ Fri, 10 Dec 2021 09:59:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723687/SRX7723687.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 09:59:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723687/SRX7723687.05_summits.bed INFO @ Fri, 10 Dec 2021 09:59:43: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3029 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 09:59:46: 8000000 INFO @ Fri, 10 Dec 2021 09:59:52: 9000000 INFO @ Fri, 10 Dec 2021 09:59:56: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 09:59:59: 10000000 INFO @ Fri, 10 Dec 2021 10:00:01: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 10:00:01: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 10:00:01: #1 total tags in treatment: 10451494 INFO @ Fri, 10 Dec 2021 10:00:01: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 10:00:01: #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 10:00:02: #1 tags after filtering in treatment: 10451494 INFO @ Fri, 10 Dec 2021 10:00:02: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 10:00:02: #1 finished! INFO @ Fri, 10 Dec 2021 10:00:02: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 10:00:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 10:00:02: #2 number of paired peaks: 484 WARNING @ Fri, 10 Dec 2021 10:00:02: Fewer paired peaks (484) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 484 pairs to build model! INFO @ Fri, 10 Dec 2021 10:00:02: start model_add_line... INFO @ Fri, 10 Dec 2021 10:00:02: start X-correlation... INFO @ Fri, 10 Dec 2021 10:00:02: end of X-cor INFO @ Fri, 10 Dec 2021 10:00:02: #2 finished! INFO @ Fri, 10 Dec 2021 10:00:02: #2 predicted fragment length is 66 bps INFO @ Fri, 10 Dec 2021 10:00:02: #2 alternative fragment length(s) may be 66 bps INFO @ Fri, 10 Dec 2021 10:00:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723687/SRX7723687.20_model.r WARNING @ Fri, 10 Dec 2021 10:00:02: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 10:00:02: #2 You may need to consider one of the other alternative d(s): 66 WARNING @ Fri, 10 Dec 2021 10:00:02: #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 10:00:02: #3 Call peaks... INFO @ Fri, 10 Dec 2021 10:00:02: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 10:00:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723687/SRX7723687.10_peaks.xls INFO @ Fri, 10 Dec 2021 10:00:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723687/SRX7723687.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 10:00:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723687/SRX7723687.10_summits.bed INFO @ Fri, 10 Dec 2021 10:00:07: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1789 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 10:00:23: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 10:00:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723687/SRX7723687.20_peaks.xls INFO @ Fri, 10 Dec 2021 10:00:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723687/SRX7723687.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 10:00:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723687/SRX7723687.20_summits.bed INFO @ Fri, 10 Dec 2021 10:00:34: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1115 records, 4 fields): 2 millis CompletedMACS2peakCalling