Job ID = 12265277 SRX = SRX5010736 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 23886047 spots for SRR8191161/SRR8191161.sra Written 23886047 spots for SRR8191161/SRR8191161.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265412 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:06:05 23886047 reads; of these: 23886047 (100.00%) were unpaired; of these: 899979 (3.77%) aligned 0 times 9007134 (37.71%) aligned exactly 1 time 13978934 (58.52%) aligned >1 times 96.23% overall alignment rate Time searching: 00:06:06 Overall time: 00:06:06 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] 14153517 / 22986068 = 0.6157 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:33:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5010736/SRX5010736.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5010736/SRX5010736.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5010736/SRX5010736.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5010736/SRX5010736.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, 03 Apr 2021 06:33:40: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:33:40: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:33:46: 1000000 INFO @ Sat, 03 Apr 2021 06:33:52: 2000000 INFO @ Sat, 03 Apr 2021 06:33:57: 3000000 INFO @ Sat, 03 Apr 2021 06:34:03: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:34:09: 5000000 INFO @ Sat, 03 Apr 2021 06:34:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5010736/SRX5010736.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5010736/SRX5010736.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5010736/SRX5010736.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5010736/SRX5010736.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, 03 Apr 2021 06:34:10: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:34:10: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:34:15: 6000000 INFO @ Sat, 03 Apr 2021 06:34:18: 1000000 INFO @ Sat, 03 Apr 2021 06:34:22: 7000000 INFO @ Sat, 03 Apr 2021 06:34:25: 2000000 INFO @ Sat, 03 Apr 2021 06:34:29: 8000000 INFO @ Sat, 03 Apr 2021 06:34:32: 3000000 INFO @ Sat, 03 Apr 2021 06:34:34: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 06:34:34: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 06:34:34: #1 total tags in treatment: 8832551 INFO @ Sat, 03 Apr 2021 06:34:34: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:34:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:34:35: #1 tags after filtering in treatment: 8832551 INFO @ Sat, 03 Apr 2021 06:34:35: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:34:35: #1 finished! INFO @ Sat, 03 Apr 2021 06:34:35: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:34:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:34:35: #2 number of paired peaks: 345 WARNING @ Sat, 03 Apr 2021 06:34:35: Fewer paired peaks (345) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 345 pairs to build model! INFO @ Sat, 03 Apr 2021 06:34:35: start model_add_line... INFO @ Sat, 03 Apr 2021 06:34:35: start X-correlation... INFO @ Sat, 03 Apr 2021 06:34:35: end of X-cor INFO @ Sat, 03 Apr 2021 06:34:35: #2 finished! INFO @ Sat, 03 Apr 2021 06:34:35: #2 predicted fragment length is 58 bps INFO @ Sat, 03 Apr 2021 06:34:35: #2 alternative fragment length(s) may be 58 bps INFO @ Sat, 03 Apr 2021 06:34:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5010736/SRX5010736.05_model.r WARNING @ Sat, 03 Apr 2021 06:34:35: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:34:35: #2 You may need to consider one of the other alternative d(s): 58 WARNING @ Sat, 03 Apr 2021 06:34:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:34:35: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:34:35: #3 Pre-compute pvalue-qvalue table... BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:34:39: 4000000 INFO @ Sat, 03 Apr 2021 06:34:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5010736/SRX5010736.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5010736/SRX5010736.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5010736/SRX5010736.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5010736/SRX5010736.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, 03 Apr 2021 06:34:40: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:34:40: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:34:47: 5000000 INFO @ Sat, 03 Apr 2021 06:34:47: 1000000 INFO @ Sat, 03 Apr 2021 06:34:54: 2000000 INFO @ Sat, 03 Apr 2021 06:34:54: 6000000 INFO @ Sat, 03 Apr 2021 06:34:56: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:35:01: 3000000 INFO @ Sat, 03 Apr 2021 06:35:01: 7000000 INFO @ Sat, 03 Apr 2021 06:35:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5010736/SRX5010736.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:35:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5010736/SRX5010736.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:35:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5010736/SRX5010736.05_summits.bed INFO @ Sat, 03 Apr 2021 06:35:07: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4003 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:35:07: 4000000 INFO @ Sat, 03 Apr 2021 06:35:09: 8000000 INFO @ Sat, 03 Apr 2021 06:35:14: 5000000 INFO @ Sat, 03 Apr 2021 06:35:15: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 06:35:15: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 06:35:15: #1 total tags in treatment: 8832551 INFO @ Sat, 03 Apr 2021 06:35:15: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:35:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:35:15: #1 tags after filtering in treatment: 8832551 INFO @ Sat, 03 Apr 2021 06:35:15: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:35:15: #1 finished! INFO @ Sat, 03 Apr 2021 06:35:15: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:35:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:35:16: #2 number of paired peaks: 345 WARNING @ Sat, 03 Apr 2021 06:35:16: Fewer paired peaks (345) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 345 pairs to build model! INFO @ Sat, 03 Apr 2021 06:35:16: start model_add_line... INFO @ Sat, 03 Apr 2021 06:35:16: start X-correlation... INFO @ Sat, 03 Apr 2021 06:35:16: end of X-cor INFO @ Sat, 03 Apr 2021 06:35:16: #2 finished! INFO @ Sat, 03 Apr 2021 06:35:16: #2 predicted fragment length is 58 bps INFO @ Sat, 03 Apr 2021 06:35:16: #2 alternative fragment length(s) may be 58 bps INFO @ Sat, 03 Apr 2021 06:35:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5010736/SRX5010736.10_model.r WARNING @ Sat, 03 Apr 2021 06:35:16: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:35:16: #2 You may need to consider one of the other alternative d(s): 58 WARNING @ Sat, 03 Apr 2021 06:35:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:35:16: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:35:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:35:20: 6000000 INFO @ Sat, 03 Apr 2021 06:35:26: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:35:32: 8000000 INFO @ Sat, 03 Apr 2021 06:35:36: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:35:37: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 06:35:37: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 06:35:37: #1 total tags in treatment: 8832551 INFO @ Sat, 03 Apr 2021 06:35:37: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:35:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:35:37: #1 tags after filtering in treatment: 8832551 INFO @ Sat, 03 Apr 2021 06:35:37: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:35:37: #1 finished! INFO @ Sat, 03 Apr 2021 06:35:37: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:35:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:35:38: #2 number of paired peaks: 345 WARNING @ Sat, 03 Apr 2021 06:35:38: Fewer paired peaks (345) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 345 pairs to build model! INFO @ Sat, 03 Apr 2021 06:35:38: start model_add_line... INFO @ Sat, 03 Apr 2021 06:35:38: start X-correlation... INFO @ Sat, 03 Apr 2021 06:35:38: end of X-cor INFO @ Sat, 03 Apr 2021 06:35:38: #2 finished! INFO @ Sat, 03 Apr 2021 06:35:38: #2 predicted fragment length is 58 bps INFO @ Sat, 03 Apr 2021 06:35:38: #2 alternative fragment length(s) may be 58 bps INFO @ Sat, 03 Apr 2021 06:35:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5010736/SRX5010736.20_model.r WARNING @ Sat, 03 Apr 2021 06:35:38: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:35:38: #2 You may need to consider one of the other alternative d(s): 58 WARNING @ Sat, 03 Apr 2021 06:35:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:35:38: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:35:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:35:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5010736/SRX5010736.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:35:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5010736/SRX5010736.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:35:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5010736/SRX5010736.10_summits.bed INFO @ Sat, 03 Apr 2021 06:35:47: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1894 records, 4 fields): 5 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 06:35:59: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:36:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5010736/SRX5010736.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:36:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5010736/SRX5010736.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:36:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5010736/SRX5010736.20_summits.bed INFO @ Sat, 03 Apr 2021 06:36:10: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (411 records, 4 fields): 2 millis CompletedMACS2peakCalling