Job ID = 14170387 SRX = SRX8784748 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 7520658 spots for SRR12280878/SRR12280878.sra Written 7520658 spots for SRR12280878/SRR12280878.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170789 ("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: 00:03:13 7520658 reads; of these: 7520658 (100.00%) were unpaired; of these: 521976 (6.94%) aligned 0 times 6090150 (80.98%) aligned exactly 1 time 908532 (12.08%) aligned >1 times 93.06% overall alignment rate Time searching: 00:03:13 Overall time: 00:03:13 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] 400439 / 6998682 = 0.0572 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 06:41:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8784748/SRX8784748.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8784748/SRX8784748.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8784748/SRX8784748.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8784748/SRX8784748.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 06:41:48: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:41:48: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:41:55: 1000000 INFO @ Sat, 11 Dec 2021 06:42:02: 2000000 INFO @ Sat, 11 Dec 2021 06:42:10: 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 @ Sat, 11 Dec 2021 06:42:17: 4000000 INFO @ Sat, 11 Dec 2021 06:42:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8784748/SRX8784748.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8784748/SRX8784748.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8784748/SRX8784748.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8784748/SRX8784748.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 06:42:17: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:42:17: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:42:25: 5000000 INFO @ Sat, 11 Dec 2021 06:42:26: 1000000 INFO @ Sat, 11 Dec 2021 06:42:34: 6000000 INFO @ Sat, 11 Dec 2021 06:42:35: 2000000 INFO @ Sat, 11 Dec 2021 06:42:40: #1 tag size is determined as 100 bps INFO @ Sat, 11 Dec 2021 06:42:40: #1 tag size = 100 INFO @ Sat, 11 Dec 2021 06:42:40: #1 total tags in treatment: 6598243 INFO @ Sat, 11 Dec 2021 06:42:40: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:42:40: #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 06:42:40: #1 tags after filtering in treatment: 6598243 INFO @ Sat, 11 Dec 2021 06:42:40: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:42:40: #1 finished! INFO @ Sat, 11 Dec 2021 06:42:40: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:42:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:42:40: #2 number of paired peaks: 155 WARNING @ Sat, 11 Dec 2021 06:42:40: Fewer paired peaks (155) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 155 pairs to build model! INFO @ Sat, 11 Dec 2021 06:42:40: start model_add_line... INFO @ Sat, 11 Dec 2021 06:42:40: start X-correlation... INFO @ Sat, 11 Dec 2021 06:42:40: end of X-cor INFO @ Sat, 11 Dec 2021 06:42:40: #2 finished! INFO @ Sat, 11 Dec 2021 06:42:40: #2 predicted fragment length is 106 bps INFO @ Sat, 11 Dec 2021 06:42:40: #2 alternative fragment length(s) may be 4,106 bps INFO @ Sat, 11 Dec 2021 06:42:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8784748/SRX8784748.05_model.r WARNING @ Sat, 11 Dec 2021 06:42:40: #2 Since the d (106) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:42:40: #2 You may need to consider one of the other alternative d(s): 4,106 WARNING @ Sat, 11 Dec 2021 06:42:40: #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 06:42:40: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:42:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:42:44: 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 @ Sat, 11 Dec 2021 06:42:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8784748/SRX8784748.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8784748/SRX8784748.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8784748/SRX8784748.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8784748/SRX8784748.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 06:42:47: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:42:47: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:42:52: 4000000 INFO @ Sat, 11 Dec 2021 06:42:54: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:42:56: 1000000 INFO @ Sat, 11 Dec 2021 06:43:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8784748/SRX8784748.05_peaks.xls INFO @ Sat, 11 Dec 2021 06:43:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8784748/SRX8784748.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:43:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8784748/SRX8784748.05_summits.bed INFO @ Sat, 11 Dec 2021 06:43:01: Done! INFO @ Sat, 11 Dec 2021 06:43:01: 5000000 pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (777 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 06:43:05: 2000000 INFO @ Sat, 11 Dec 2021 06:43:10: 6000000 INFO @ Sat, 11 Dec 2021 06:43:14: 3000000 INFO @ Sat, 11 Dec 2021 06:43:15: #1 tag size is determined as 100 bps INFO @ Sat, 11 Dec 2021 06:43:15: #1 tag size = 100 INFO @ Sat, 11 Dec 2021 06:43:15: #1 total tags in treatment: 6598243 INFO @ Sat, 11 Dec 2021 06:43:15: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:43:15: #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 06:43:15: #1 tags after filtering in treatment: 6598243 INFO @ Sat, 11 Dec 2021 06:43:15: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:43:15: #1 finished! INFO @ Sat, 11 Dec 2021 06:43:15: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:43:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:43:15: #2 number of paired peaks: 155 WARNING @ Sat, 11 Dec 2021 06:43:15: Fewer paired peaks (155) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 155 pairs to build model! INFO @ Sat, 11 Dec 2021 06:43:15: start model_add_line... INFO @ Sat, 11 Dec 2021 06:43:16: start X-correlation... INFO @ Sat, 11 Dec 2021 06:43:16: end of X-cor INFO @ Sat, 11 Dec 2021 06:43:16: #2 finished! INFO @ Sat, 11 Dec 2021 06:43:16: #2 predicted fragment length is 106 bps INFO @ Sat, 11 Dec 2021 06:43:16: #2 alternative fragment length(s) may be 4,106 bps INFO @ Sat, 11 Dec 2021 06:43:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8784748/SRX8784748.10_model.r WARNING @ Sat, 11 Dec 2021 06:43:16: #2 Since the d (106) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:43:16: #2 You may need to consider one of the other alternative d(s): 4,106 WARNING @ Sat, 11 Dec 2021 06:43:16: #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 06:43:16: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:43:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:43:21: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 06:43:29: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:43:29: 5000000 INFO @ Sat, 11 Dec 2021 06:43:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8784748/SRX8784748.10_peaks.xls INFO @ Sat, 11 Dec 2021 06:43:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8784748/SRX8784748.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:43:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8784748/SRX8784748.10_summits.bed INFO @ Sat, 11 Dec 2021 06:43:35: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (222 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 06:43:37: 6000000 INFO @ Sat, 11 Dec 2021 06:43:41: #1 tag size is determined as 100 bps INFO @ Sat, 11 Dec 2021 06:43:41: #1 tag size = 100 INFO @ Sat, 11 Dec 2021 06:43:41: #1 total tags in treatment: 6598243 INFO @ Sat, 11 Dec 2021 06:43:41: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:43:41: #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 06:43:41: #1 tags after filtering in treatment: 6598243 INFO @ Sat, 11 Dec 2021 06:43:41: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:43:41: #1 finished! INFO @ Sat, 11 Dec 2021 06:43:41: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:43:41: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 06:43:42: #2 number of paired peaks: 155 WARNING @ Sat, 11 Dec 2021 06:43:42: Fewer paired peaks (155) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 155 pairs to build model! INFO @ Sat, 11 Dec 2021 06:43:42: start model_add_line... INFO @ Sat, 11 Dec 2021 06:43:42: start X-correlation... INFO @ Sat, 11 Dec 2021 06:43:42: end of X-cor INFO @ Sat, 11 Dec 2021 06:43:42: #2 finished! INFO @ Sat, 11 Dec 2021 06:43:42: #2 predicted fragment length is 106 bps INFO @ Sat, 11 Dec 2021 06:43:42: #2 alternative fragment length(s) may be 4,106 bps INFO @ Sat, 11 Dec 2021 06:43:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8784748/SRX8784748.20_model.r WARNING @ Sat, 11 Dec 2021 06:43:42: #2 Since the d (106) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:43:42: #2 You may need to consider one of the other alternative d(s): 4,106 WARNING @ Sat, 11 Dec 2021 06:43:42: #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 06:43:42: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:43:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:43:55: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:44:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8784748/SRX8784748.20_peaks.xls INFO @ Sat, 11 Dec 2021 06:44:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8784748/SRX8784748.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:44:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8784748/SRX8784748.20_summits.bed INFO @ Sat, 11 Dec 2021 06:44:02: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (75 records, 4 fields): 1 millis CompletedMACS2peakCalling