Job ID = 6529594 SRX = SRX331404 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:30 23568994 reads; of these: 23568994 (100.00%) were unpaired; of these: 1622457 (6.88%) aligned 0 times 15669484 (66.48%) aligned exactly 1 time 6277053 (26.63%) aligned >1 times 93.12% overall alignment rate Time searching: 00:06:30 Overall time: 00:06:30 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 4917179 / 21946537 = 0.2241 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, 30 Jun 2020 02:47:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX331404/SRX331404.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX331404/SRX331404.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX331404/SRX331404.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX331404/SRX331404.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, 30 Jun 2020 02:47:01: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:47:01: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:47:10: 1000000 INFO @ Tue, 30 Jun 2020 02:47:18: 2000000 INFO @ Tue, 30 Jun 2020 02:47:27: 3000000 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, 30 Jun 2020 02:47:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX331404/SRX331404.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX331404/SRX331404.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX331404/SRX331404.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX331404/SRX331404.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, 30 Jun 2020 02:47:31: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:47:31: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:47:35: 4000000 INFO @ Tue, 30 Jun 2020 02:47:39: 1000000 INFO @ Tue, 30 Jun 2020 02:47:44: 5000000 INFO @ Tue, 30 Jun 2020 02:47:48: 2000000 INFO @ Tue, 30 Jun 2020 02:47:53: 6000000 INFO @ Tue, 30 Jun 2020 02:47:56: 3000000 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, 30 Jun 2020 02:48:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX331404/SRX331404.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX331404/SRX331404.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX331404/SRX331404.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX331404/SRX331404.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, 30 Jun 2020 02:48:01: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:48:01: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:48:02: 7000000 INFO @ Tue, 30 Jun 2020 02:48:04: 4000000 INFO @ Tue, 30 Jun 2020 02:48:11: 1000000 INFO @ Tue, 30 Jun 2020 02:48:12: 8000000 INFO @ Tue, 30 Jun 2020 02:48:13: 5000000 INFO @ Tue, 30 Jun 2020 02:48:20: 2000000 INFO @ Tue, 30 Jun 2020 02:48:21: 9000000 INFO @ Tue, 30 Jun 2020 02:48:22: 6000000 INFO @ Tue, 30 Jun 2020 02:48:29: 3000000 INFO @ Tue, 30 Jun 2020 02:48:30: 7000000 INFO @ Tue, 30 Jun 2020 02:48:31: 10000000 INFO @ Tue, 30 Jun 2020 02:48:39: 4000000 INFO @ Tue, 30 Jun 2020 02:48:39: 8000000 INFO @ Tue, 30 Jun 2020 02:48:40: 11000000 INFO @ Tue, 30 Jun 2020 02:48:48: 9000000 INFO @ Tue, 30 Jun 2020 02:48:48: 5000000 INFO @ Tue, 30 Jun 2020 02:48:49: 12000000 INFO @ Tue, 30 Jun 2020 02:48:57: 10000000 INFO @ Tue, 30 Jun 2020 02:48:57: 6000000 INFO @ Tue, 30 Jun 2020 02:48:59: 13000000 INFO @ Tue, 30 Jun 2020 02:49:05: 11000000 INFO @ Tue, 30 Jun 2020 02:49:06: 7000000 INFO @ Tue, 30 Jun 2020 02:49:09: 14000000 INFO @ Tue, 30 Jun 2020 02:49:14: 12000000 INFO @ Tue, 30 Jun 2020 02:49:16: 8000000 INFO @ Tue, 30 Jun 2020 02:49:19: 15000000 INFO @ Tue, 30 Jun 2020 02:49:22: 13000000 INFO @ Tue, 30 Jun 2020 02:49:25: 9000000 INFO @ Tue, 30 Jun 2020 02:49:28: 16000000 INFO @ Tue, 30 Jun 2020 02:49:32: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:49:35: 10000000 INFO @ Tue, 30 Jun 2020 02:49:38: 17000000 INFO @ Tue, 30 Jun 2020 02:49:38: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:49:38: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:49:38: #1 total tags in treatment: 17029358 INFO @ Tue, 30 Jun 2020 02:49:38: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:49:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:49:39: #1 tags after filtering in treatment: 17029357 INFO @ Tue, 30 Jun 2020 02:49:39: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:49:39: #1 finished! INFO @ Tue, 30 Jun 2020 02:49:39: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:49:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:49:40: 15000000 INFO @ Tue, 30 Jun 2020 02:49:40: #2 number of paired peaks: 430 WARNING @ Tue, 30 Jun 2020 02:49:40: Fewer paired peaks (430) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 430 pairs to build model! INFO @ Tue, 30 Jun 2020 02:49:40: start model_add_line... INFO @ Tue, 30 Jun 2020 02:49:40: start X-correlation... INFO @ Tue, 30 Jun 2020 02:49:40: end of X-cor INFO @ Tue, 30 Jun 2020 02:49:40: #2 finished! INFO @ Tue, 30 Jun 2020 02:49:40: #2 predicted fragment length is 50 bps INFO @ Tue, 30 Jun 2020 02:49:40: #2 alternative fragment length(s) may be 2,50,590,597 bps INFO @ Tue, 30 Jun 2020 02:49:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX331404/SRX331404.05_model.r WARNING @ Tue, 30 Jun 2020 02:49:40: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:49:40: #2 You may need to consider one of the other alternative d(s): 2,50,590,597 WARNING @ Tue, 30 Jun 2020 02:49:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:49:40: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:49:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:49:44: 11000000 INFO @ Tue, 30 Jun 2020 02:49:49: 16000000 INFO @ Tue, 30 Jun 2020 02:49:52: 12000000 INFO @ Tue, 30 Jun 2020 02:49:57: 17000000 INFO @ Tue, 30 Jun 2020 02:49:58: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:49:58: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:49:58: #1 total tags in treatment: 17029358 INFO @ Tue, 30 Jun 2020 02:49:58: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:49:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:49:58: #1 tags after filtering in treatment: 17029357 INFO @ Tue, 30 Jun 2020 02:49:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:49:58: #1 finished! INFO @ Tue, 30 Jun 2020 02:49:58: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:49:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:50:00: #2 number of paired peaks: 430 WARNING @ Tue, 30 Jun 2020 02:50:00: Fewer paired peaks (430) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 430 pairs to build model! INFO @ Tue, 30 Jun 2020 02:50:00: start model_add_line... INFO @ Tue, 30 Jun 2020 02:50:00: start X-correlation... INFO @ Tue, 30 Jun 2020 02:50:00: end of X-cor INFO @ Tue, 30 Jun 2020 02:50:00: #2 finished! INFO @ Tue, 30 Jun 2020 02:50:00: #2 predicted fragment length is 50 bps INFO @ Tue, 30 Jun 2020 02:50:00: #2 alternative fragment length(s) may be 2,50,590,597 bps INFO @ Tue, 30 Jun 2020 02:50:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX331404/SRX331404.10_model.r WARNING @ Tue, 30 Jun 2020 02:50:00: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:50:00: #2 You may need to consider one of the other alternative d(s): 2,50,590,597 WARNING @ Tue, 30 Jun 2020 02:50:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:50:00: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:50:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:50:01: 13000000 INFO @ Tue, 30 Jun 2020 02:50:10: 14000000 INFO @ Tue, 30 Jun 2020 02:50:11: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:50:19: 15000000 BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:50:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX331404/SRX331404.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:50:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX331404/SRX331404.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:50:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX331404/SRX331404.05_summits.bed INFO @ Tue, 30 Jun 2020 02:50:26: Done! pass1 - making usageList (587 chroms): 1 millis pass2 - checking and writing primary data (2294 records, 4 fields): 35 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:50:28: 16000000 INFO @ Tue, 30 Jun 2020 02:50:30: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:50:37: 17000000 INFO @ Tue, 30 Jun 2020 02:50:37: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:50:37: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:50:37: #1 total tags in treatment: 17029358 INFO @ Tue, 30 Jun 2020 02:50:37: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:50:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:50:38: #1 tags after filtering in treatment: 17029357 INFO @ Tue, 30 Jun 2020 02:50:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:50:38: #1 finished! INFO @ Tue, 30 Jun 2020 02:50:38: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:50:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:50:39: #2 number of paired peaks: 430 WARNING @ Tue, 30 Jun 2020 02:50:39: Fewer paired peaks (430) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 430 pairs to build model! INFO @ Tue, 30 Jun 2020 02:50:39: start model_add_line... INFO @ Tue, 30 Jun 2020 02:50:39: start X-correlation... INFO @ Tue, 30 Jun 2020 02:50:39: end of X-cor INFO @ Tue, 30 Jun 2020 02:50:39: #2 finished! INFO @ Tue, 30 Jun 2020 02:50:39: #2 predicted fragment length is 50 bps INFO @ Tue, 30 Jun 2020 02:50:39: #2 alternative fragment length(s) may be 2,50,590,597 bps INFO @ Tue, 30 Jun 2020 02:50:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX331404/SRX331404.20_model.r WARNING @ Tue, 30 Jun 2020 02:50:39: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:50:39: #2 You may need to consider one of the other alternative d(s): 2,50,590,597 WARNING @ Tue, 30 Jun 2020 02:50:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:50:39: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:50:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:50:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX331404/SRX331404.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:50:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX331404/SRX331404.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:50:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX331404/SRX331404.10_summits.bed INFO @ Tue, 30 Jun 2020 02:50:45: Done! pass1 - making usageList (348 chroms): 1 millis pass2 - checking and writing primary data (1166 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:51:10: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:51:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX331404/SRX331404.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:51:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX331404/SRX331404.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:51:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX331404/SRX331404.20_summits.bed INFO @ Tue, 30 Jun 2020 02:51:25: Done! pass1 - making usageList (216 chroms): 1 millis pass2 - checking and writing primary data (482 records, 4 fields): 13 millis CompletedMACS2peakCalling