Job ID = 12265309 SRX = SRX5010768 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 27549490 spots for SRR8191193/SRR8191193.sra Written 27549490 spots for SRR8191193/SRR8191193.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265469 ("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: 00:07:32 27549490 reads; of these: 27549490 (100.00%) were unpaired; of these: 1262330 (4.58%) aligned 0 times 12374785 (44.92%) aligned exactly 1 time 13912375 (50.50%) aligned >1 times 95.42% overall alignment rate Time searching: 00:07:32 Overall time: 00:07:32 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] 15398206 / 26287160 = 0.5858 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 06:46:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5010768/SRX5010768.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5010768/SRX5010768.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5010768/SRX5010768.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5010768/SRX5010768.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 06:46:43: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:46:43: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:46:49: 1000000 INFO @ Sat, 03 Apr 2021 06:46:54: 2000000 INFO @ Sat, 03 Apr 2021 06:46:59: 3000000 INFO @ Sat, 03 Apr 2021 06:47:05: 4000000 INFO @ Sat, 03 Apr 2021 06:47:10: 5000000 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 06:47:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5010768/SRX5010768.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5010768/SRX5010768.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5010768/SRX5010768.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5010768/SRX5010768.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 06:47:13: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:47:13: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:47:16: 6000000 INFO @ Sat, 03 Apr 2021 06:47:19: 1000000 INFO @ Sat, 03 Apr 2021 06:47:22: 7000000 INFO @ Sat, 03 Apr 2021 06:47:25: 2000000 INFO @ Sat, 03 Apr 2021 06:47:27: 8000000 INFO @ Sat, 03 Apr 2021 06:47:30: 3000000 INFO @ Sat, 03 Apr 2021 06:47:33: 9000000 INFO @ Sat, 03 Apr 2021 06:47:36: 4000000 INFO @ Sat, 03 Apr 2021 06:47:38: 10000000 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 06:47:42: 5000000 INFO @ Sat, 03 Apr 2021 06:47:43: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 06:47:43: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 06:47:43: #1 total tags in treatment: 10888954 INFO @ Sat, 03 Apr 2021 06:47:43: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:47:43: #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 06:47:43: #1 tags after filtering in treatment: 10888954 INFO @ Sat, 03 Apr 2021 06:47:43: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:47:43: #1 finished! INFO @ Sat, 03 Apr 2021 06:47:43: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:47:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:47:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5010768/SRX5010768.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5010768/SRX5010768.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5010768/SRX5010768.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5010768/SRX5010768.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 06:47:44: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:47:44: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:47:44: #2 number of paired peaks: 352 WARNING @ Sat, 03 Apr 2021 06:47:44: Fewer paired peaks (352) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 352 pairs to build model! INFO @ Sat, 03 Apr 2021 06:47:44: start model_add_line... INFO @ Sat, 03 Apr 2021 06:47:44: start X-correlation... INFO @ Sat, 03 Apr 2021 06:47:44: end of X-cor INFO @ Sat, 03 Apr 2021 06:47:44: #2 finished! INFO @ Sat, 03 Apr 2021 06:47:44: #2 predicted fragment length is 56 bps INFO @ Sat, 03 Apr 2021 06:47:44: #2 alternative fragment length(s) may be 4,56 bps INFO @ Sat, 03 Apr 2021 06:47:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5010768/SRX5010768.05_model.r WARNING @ Sat, 03 Apr 2021 06:47:44: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:47:44: #2 You may need to consider one of the other alternative d(s): 4,56 WARNING @ Sat, 03 Apr 2021 06:47:44: #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 06:47:44: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:47:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:47:48: 6000000 INFO @ Sat, 03 Apr 2021 06:47:49: 1000000 INFO @ Sat, 03 Apr 2021 06:47:53: 7000000 INFO @ Sat, 03 Apr 2021 06:47:56: 2000000 INFO @ Sat, 03 Apr 2021 06:48:00: 8000000 INFO @ Sat, 03 Apr 2021 06:48:02: 3000000 INFO @ Sat, 03 Apr 2021 06:48:05: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:48:06: 9000000 INFO @ Sat, 03 Apr 2021 06:48:09: 4000000 INFO @ Sat, 03 Apr 2021 06:48:12: 10000000 INFO @ Sat, 03 Apr 2021 06:48:15: 5000000 INFO @ Sat, 03 Apr 2021 06:48:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5010768/SRX5010768.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:48:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5010768/SRX5010768.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:48:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5010768/SRX5010768.05_summits.bed INFO @ Sat, 03 Apr 2021 06:48:17: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4550 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:48:18: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 06:48:18: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 06:48:18: #1 total tags in treatment: 10888954 INFO @ Sat, 03 Apr 2021 06:48:18: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:48:18: #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 06:48:18: #1 tags after filtering in treatment: 10888954 INFO @ Sat, 03 Apr 2021 06:48:18: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:48:18: #1 finished! INFO @ Sat, 03 Apr 2021 06:48:18: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:48:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:48:19: #2 number of paired peaks: 352 WARNING @ Sat, 03 Apr 2021 06:48:19: Fewer paired peaks (352) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 352 pairs to build model! INFO @ Sat, 03 Apr 2021 06:48:19: start model_add_line... INFO @ Sat, 03 Apr 2021 06:48:19: start X-correlation... INFO @ Sat, 03 Apr 2021 06:48:19: end of X-cor INFO @ Sat, 03 Apr 2021 06:48:19: #2 finished! INFO @ Sat, 03 Apr 2021 06:48:19: #2 predicted fragment length is 56 bps INFO @ Sat, 03 Apr 2021 06:48:19: #2 alternative fragment length(s) may be 4,56 bps INFO @ Sat, 03 Apr 2021 06:48:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5010768/SRX5010768.10_model.r WARNING @ Sat, 03 Apr 2021 06:48:19: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:48:19: #2 You may need to consider one of the other alternative d(s): 4,56 WARNING @ Sat, 03 Apr 2021 06:48:19: #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 06:48:19: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:48:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:48:21: 6000000 INFO @ Sat, 03 Apr 2021 06:48:27: 7000000 INFO @ Sat, 03 Apr 2021 06:48:33: 8000000 INFO @ Sat, 03 Apr 2021 06:48:38: 9000000 INFO @ Sat, 03 Apr 2021 06:48:39: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:48:44: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:48:48: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 06:48:48: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 06:48:48: #1 total tags in treatment: 10888954 INFO @ Sat, 03 Apr 2021 06:48:48: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:48:48: #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 06:48:49: #1 tags after filtering in treatment: 10888954 INFO @ Sat, 03 Apr 2021 06:48:49: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:48:49: #1 finished! INFO @ Sat, 03 Apr 2021 06:48:49: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:48:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:48:49: #2 number of paired peaks: 352 WARNING @ Sat, 03 Apr 2021 06:48:49: Fewer paired peaks (352) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 352 pairs to build model! INFO @ Sat, 03 Apr 2021 06:48:49: start model_add_line... INFO @ Sat, 03 Apr 2021 06:48:50: start X-correlation... INFO @ Sat, 03 Apr 2021 06:48:50: end of X-cor INFO @ Sat, 03 Apr 2021 06:48:50: #2 finished! INFO @ Sat, 03 Apr 2021 06:48:50: #2 predicted fragment length is 56 bps INFO @ Sat, 03 Apr 2021 06:48:50: #2 alternative fragment length(s) may be 4,56 bps INFO @ Sat, 03 Apr 2021 06:48:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5010768/SRX5010768.20_model.r WARNING @ Sat, 03 Apr 2021 06:48:50: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:48:50: #2 You may need to consider one of the other alternative d(s): 4,56 WARNING @ Sat, 03 Apr 2021 06:48:50: #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 06:48:50: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:48:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:48:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5010768/SRX5010768.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:48:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5010768/SRX5010768.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:48:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5010768/SRX5010768.10_summits.bed INFO @ Sat, 03 Apr 2021 06:48:50: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2145 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:49:10: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 06:49:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5010768/SRX5010768.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:49:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5010768/SRX5010768.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:49:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5010768/SRX5010768.20_summits.bed INFO @ Sat, 03 Apr 2021 06:49:21: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (417 records, 4 fields): 2 millis CompletedMACS2peakCalling