Job ID = 6626757 SRX = SRX7569434 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 25162813 spots for SRR10901256/SRR10901256.sra Written 25162813 spots for SRR10901256/SRR10901256.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627030 ("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: 00:08:06 25162813 reads; of these: 25162813 (100.00%) were unpaired; of these: 1368438 (5.44%) aligned 0 times 16619361 (66.05%) aligned exactly 1 time 7175014 (28.51%) aligned >1 times 94.56% overall alignment rate Time searching: 00:08:06 Overall time: 00:08:06 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] 5652642 / 23794375 = 0.2376 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 08:51:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7569434/SRX7569434.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7569434/SRX7569434.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7569434/SRX7569434.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7569434/SRX7569434.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 @ Tue, 14 Jul 2020 08:51:56: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:51:56: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:52:01: 1000000 INFO @ Tue, 14 Jul 2020 08:52:06: 2000000 INFO @ Tue, 14 Jul 2020 08:52:11: 3000000 INFO @ Tue, 14 Jul 2020 08:52:15: 4000000 INFO @ Tue, 14 Jul 2020 08:52:20: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 08:52:25: 6000000 INFO @ Tue, 14 Jul 2020 08:52:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7569434/SRX7569434.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7569434/SRX7569434.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7569434/SRX7569434.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7569434/SRX7569434.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 @ Tue, 14 Jul 2020 08:52:26: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:52:26: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:52:31: 7000000 INFO @ Tue, 14 Jul 2020 08:52:31: 1000000 INFO @ Tue, 14 Jul 2020 08:52:36: 8000000 INFO @ Tue, 14 Jul 2020 08:52:36: 2000000 INFO @ Tue, 14 Jul 2020 08:52:41: 9000000 INFO @ Tue, 14 Jul 2020 08:52:41: 3000000 INFO @ Tue, 14 Jul 2020 08:52:46: 10000000 INFO @ Tue, 14 Jul 2020 08:52:46: 4000000 INFO @ Tue, 14 Jul 2020 08:52:52: 11000000 INFO @ Tue, 14 Jul 2020 08:52:52: 5000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 14 Jul 2020 08:52:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7569434/SRX7569434.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7569434/SRX7569434.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7569434/SRX7569434.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7569434/SRX7569434.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 @ Tue, 14 Jul 2020 08:52:56: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:52:56: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:52:57: 12000000 INFO @ Tue, 14 Jul 2020 08:52:57: 6000000 INFO @ Tue, 14 Jul 2020 08:53:01: 1000000 INFO @ Tue, 14 Jul 2020 08:53:02: 13000000 INFO @ Tue, 14 Jul 2020 08:53:02: 7000000 INFO @ Tue, 14 Jul 2020 08:53:06: 2000000 INFO @ Tue, 14 Jul 2020 08:53:08: 14000000 INFO @ Tue, 14 Jul 2020 08:53:08: 8000000 INFO @ Tue, 14 Jul 2020 08:53:12: 3000000 INFO @ Tue, 14 Jul 2020 08:53:13: 9000000 INFO @ Tue, 14 Jul 2020 08:53:13: 15000000 INFO @ Tue, 14 Jul 2020 08:53:17: 4000000 INFO @ Tue, 14 Jul 2020 08:53:18: 10000000 INFO @ Tue, 14 Jul 2020 08:53:20: 16000000 INFO @ Tue, 14 Jul 2020 08:53:22: 5000000 INFO @ Tue, 14 Jul 2020 08:53:24: 11000000 INFO @ Tue, 14 Jul 2020 08:53:27: 17000000 INFO @ Tue, 14 Jul 2020 08:53:28: 6000000 INFO @ Tue, 14 Jul 2020 08:53:29: 12000000 INFO @ Tue, 14 Jul 2020 08:53:33: 7000000 INFO @ Tue, 14 Jul 2020 08:53:33: 18000000 INFO @ Tue, 14 Jul 2020 08:53:34: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 08:53:34: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 08:53:34: #1 total tags in treatment: 18141733 INFO @ Tue, 14 Jul 2020 08:53:34: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:53:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 08:53:34: #1 tags after filtering in treatment: 18141733 INFO @ Tue, 14 Jul 2020 08:53:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 08:53:34: #1 finished! INFO @ Tue, 14 Jul 2020 08:53:34: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:53:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:53:35: 13000000 INFO @ Tue, 14 Jul 2020 08:53:35: #2 number of paired peaks: 103 WARNING @ Tue, 14 Jul 2020 08:53:35: Fewer paired peaks (103) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 103 pairs to build model! INFO @ Tue, 14 Jul 2020 08:53:35: start model_add_line... INFO @ Tue, 14 Jul 2020 08:53:36: start X-correlation... INFO @ Tue, 14 Jul 2020 08:53:36: end of X-cor INFO @ Tue, 14 Jul 2020 08:53:36: #2 finished! INFO @ Tue, 14 Jul 2020 08:53:36: #2 predicted fragment length is 55 bps INFO @ Tue, 14 Jul 2020 08:53:36: #2 alternative fragment length(s) may be 3,37,55,102,164,214,229,358,433,461,482,556 bps INFO @ Tue, 14 Jul 2020 08:53:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7569434/SRX7569434.05_model.r WARNING @ Tue, 14 Jul 2020 08:53:36: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:53:36: #2 You may need to consider one of the other alternative d(s): 3,37,55,102,164,214,229,358,433,461,482,556 WARNING @ Tue, 14 Jul 2020 08:53:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 08:53:36: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:53:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:53:38: 8000000 INFO @ Tue, 14 Jul 2020 08:53:40: 14000000 INFO @ Tue, 14 Jul 2020 08:53:43: 9000000 INFO @ Tue, 14 Jul 2020 08:53:45: 15000000 INFO @ Tue, 14 Jul 2020 08:53:49: 10000000 INFO @ Tue, 14 Jul 2020 08:53:51: 16000000 INFO @ Tue, 14 Jul 2020 08:53:54: 11000000 INFO @ Tue, 14 Jul 2020 08:53:56: 17000000 INFO @ Tue, 14 Jul 2020 08:53:59: 12000000 INFO @ Tue, 14 Jul 2020 08:54:01: 18000000 INFO @ Tue, 14 Jul 2020 08:54:02: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 08:54:02: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 08:54:02: #1 total tags in treatment: 18141733 INFO @ Tue, 14 Jul 2020 08:54:02: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:54:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 08:54:02: #1 tags after filtering in treatment: 18141733 INFO @ Tue, 14 Jul 2020 08:54:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 08:54:02: #1 finished! INFO @ Tue, 14 Jul 2020 08:54:02: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:54:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:54:04: #2 number of paired peaks: 103 WARNING @ Tue, 14 Jul 2020 08:54:04: Fewer paired peaks (103) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 103 pairs to build model! INFO @ Tue, 14 Jul 2020 08:54:04: start model_add_line... INFO @ Tue, 14 Jul 2020 08:54:04: start X-correlation... INFO @ Tue, 14 Jul 2020 08:54:04: end of X-cor INFO @ Tue, 14 Jul 2020 08:54:04: #2 finished! INFO @ Tue, 14 Jul 2020 08:54:04: #2 predicted fragment length is 55 bps INFO @ Tue, 14 Jul 2020 08:54:04: #2 alternative fragment length(s) may be 3,37,55,102,164,214,229,358,433,461,482,556 bps INFO @ Tue, 14 Jul 2020 08:54:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7569434/SRX7569434.10_model.r WARNING @ Tue, 14 Jul 2020 08:54:04: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:54:04: #2 You may need to consider one of the other alternative d(s): 3,37,55,102,164,214,229,358,433,461,482,556 WARNING @ Tue, 14 Jul 2020 08:54:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 08:54:04: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:54:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:54:05: 13000000 INFO @ Tue, 14 Jul 2020 08:54:10: 14000000 INFO @ Tue, 14 Jul 2020 08:54:10: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:54:15: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 08:54:20: 16000000 INFO @ Tue, 14 Jul 2020 08:54:25: 17000000 INFO @ Tue, 14 Jul 2020 08:54:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7569434/SRX7569434.05_peaks.xls INFO @ Tue, 14 Jul 2020 08:54:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7569434/SRX7569434.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:54:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7569434/SRX7569434.05_summits.bed INFO @ Tue, 14 Jul 2020 08:54:28: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2425 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 08:54:30: 18000000 INFO @ Tue, 14 Jul 2020 08:54:31: #1 tag size is determined as 50 bps INFO @ Tue, 14 Jul 2020 08:54:31: #1 tag size = 50 INFO @ Tue, 14 Jul 2020 08:54:31: #1 total tags in treatment: 18141733 INFO @ Tue, 14 Jul 2020 08:54:31: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:54:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 08:54:32: #1 tags after filtering in treatment: 18141733 INFO @ Tue, 14 Jul 2020 08:54:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 08:54:32: #1 finished! INFO @ Tue, 14 Jul 2020 08:54:32: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:54:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:54:33: #2 number of paired peaks: 103 WARNING @ Tue, 14 Jul 2020 08:54:33: Fewer paired peaks (103) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 103 pairs to build model! INFO @ Tue, 14 Jul 2020 08:54:33: start model_add_line... INFO @ Tue, 14 Jul 2020 08:54:33: start X-correlation... INFO @ Tue, 14 Jul 2020 08:54:33: end of X-cor INFO @ Tue, 14 Jul 2020 08:54:33: #2 finished! INFO @ Tue, 14 Jul 2020 08:54:33: #2 predicted fragment length is 55 bps INFO @ Tue, 14 Jul 2020 08:54:33: #2 alternative fragment length(s) may be 3,37,55,102,164,214,229,358,433,461,482,556 bps INFO @ Tue, 14 Jul 2020 08:54:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7569434/SRX7569434.20_model.r WARNING @ Tue, 14 Jul 2020 08:54:33: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:54:33: #2 You may need to consider one of the other alternative d(s): 3,37,55,102,164,214,229,358,433,461,482,556 WARNING @ Tue, 14 Jul 2020 08:54:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 08:54:33: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:54:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:54:37: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:54:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7569434/SRX7569434.10_peaks.xls INFO @ Tue, 14 Jul 2020 08:54:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7569434/SRX7569434.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:54:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7569434/SRX7569434.10_summits.bed INFO @ Tue, 14 Jul 2020 08:54:54: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1204 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 08:55:06: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:55:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7569434/SRX7569434.20_peaks.xls INFO @ Tue, 14 Jul 2020 08:55:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7569434/SRX7569434.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:55:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7569434/SRX7569434.20_summits.bed INFO @ Tue, 14 Jul 2020 08:55:23: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (208 records, 4 fields): 22 millis CompletedMACS2peakCalling