Job ID = 6626621 SRX = SRX5734949 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: 00:08:31 20681321 reads; of these: 20681321 (100.00%) were unpaired; of these: 1471962 (7.12%) aligned 0 times 15811996 (76.46%) aligned exactly 1 time 3397363 (16.43%) aligned >1 times 92.88% overall alignment rate Time searching: 00:08:31 Overall time: 00:08:31 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 8 files... [bam_rmdupse_core] 8915564 / 19209359 = 0.4641 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 08:10:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5734949/SRX5734949.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5734949/SRX5734949.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5734949/SRX5734949.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5734949/SRX5734949.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 08:10:33: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:10:33: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:10:38: 1000000 INFO @ Tue, 14 Jul 2020 08:10:44: 2000000 INFO @ Tue, 14 Jul 2020 08:10:49: 3000000 INFO @ Tue, 14 Jul 2020 08:10:54: 4000000 INFO @ Tue, 14 Jul 2020 08:10:59: 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 08:11:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5734949/SRX5734949.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5734949/SRX5734949.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5734949/SRX5734949.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5734949/SRX5734949.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 08:11:03: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:11:03: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:11:04: 6000000 INFO @ Tue, 14 Jul 2020 08:11:08: 1000000 INFO @ Tue, 14 Jul 2020 08:11:09: 7000000 INFO @ Tue, 14 Jul 2020 08:11:14: 2000000 INFO @ Tue, 14 Jul 2020 08:11:15: 8000000 INFO @ Tue, 14 Jul 2020 08:11:19: 3000000 INFO @ Tue, 14 Jul 2020 08:11:20: 9000000 INFO @ Tue, 14 Jul 2020 08:11:24: 4000000 INFO @ Tue, 14 Jul 2020 08:11:25: 10000000 INFO @ Tue, 14 Jul 2020 08:11:26: #1 tag size is determined as 78 bps INFO @ Tue, 14 Jul 2020 08:11:26: #1 tag size = 78 INFO @ Tue, 14 Jul 2020 08:11:26: #1 total tags in treatment: 10293795 INFO @ Tue, 14 Jul 2020 08:11:26: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:11:26: #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 08:11:27: #1 tags after filtering in treatment: 10293535 INFO @ Tue, 14 Jul 2020 08:11:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 08:11:27: #1 finished! INFO @ Tue, 14 Jul 2020 08:11:27: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:11:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:11:28: #2 number of paired peaks: 3579 INFO @ Tue, 14 Jul 2020 08:11:28: start model_add_line... INFO @ Tue, 14 Jul 2020 08:11:28: start X-correlation... INFO @ Tue, 14 Jul 2020 08:11:28: end of X-cor INFO @ Tue, 14 Jul 2020 08:11:28: #2 finished! INFO @ Tue, 14 Jul 2020 08:11:28: #2 predicted fragment length is 2 bps INFO @ Tue, 14 Jul 2020 08:11:28: #2 alternative fragment length(s) may be 2 bps INFO @ Tue, 14 Jul 2020 08:11:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5734949/SRX5734949.05_model.r WARNING @ Tue, 14 Jul 2020 08:11:28: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:11:28: #2 You may need to consider one of the other alternative d(s): 2 WARNING @ Tue, 14 Jul 2020 08:11:28: #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 08:11:28: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:11:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:11:29: 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 08:11:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5734949/SRX5734949.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5734949/SRX5734949.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5734949/SRX5734949.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5734949/SRX5734949.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 08:11:33: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:11:33: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:11:35: 6000000 INFO @ Tue, 14 Jul 2020 08:11:39: 1000000 INFO @ Tue, 14 Jul 2020 08:11:40: 7000000 INFO @ Tue, 14 Jul 2020 08:11:44: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:11:44: 2000000 INFO @ Tue, 14 Jul 2020 08:11:45: 8000000 INFO @ Tue, 14 Jul 2020 08:11:49: 3000000 INFO @ Tue, 14 Jul 2020 08:11:50: 9000000 INFO @ Tue, 14 Jul 2020 08:11:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5734949/SRX5734949.05_peaks.xls INFO @ Tue, 14 Jul 2020 08:11:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5734949/SRX5734949.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:11:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5734949/SRX5734949.05_summits.bed INFO @ Tue, 14 Jul 2020 08:11:51: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 08:11:55: 4000000 INFO @ Tue, 14 Jul 2020 08:11:56: 10000000 INFO @ Tue, 14 Jul 2020 08:11:57: #1 tag size is determined as 78 bps INFO @ Tue, 14 Jul 2020 08:11:57: #1 tag size = 78 INFO @ Tue, 14 Jul 2020 08:11:57: #1 total tags in treatment: 10293795 INFO @ Tue, 14 Jul 2020 08:11:57: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:11:57: #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 08:11:58: #1 tags after filtering in treatment: 10293535 INFO @ Tue, 14 Jul 2020 08:11:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 08:11:58: #1 finished! INFO @ Tue, 14 Jul 2020 08:11:58: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:11:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:11:59: #2 number of paired peaks: 3579 INFO @ Tue, 14 Jul 2020 08:11:59: start model_add_line... INFO @ Tue, 14 Jul 2020 08:11:59: start X-correlation... INFO @ Tue, 14 Jul 2020 08:11:59: end of X-cor INFO @ Tue, 14 Jul 2020 08:11:59: #2 finished! INFO @ Tue, 14 Jul 2020 08:11:59: #2 predicted fragment length is 2 bps INFO @ Tue, 14 Jul 2020 08:11:59: #2 alternative fragment length(s) may be 2 bps INFO @ Tue, 14 Jul 2020 08:11:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5734949/SRX5734949.10_model.r WARNING @ Tue, 14 Jul 2020 08:11:59: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:11:59: #2 You may need to consider one of the other alternative d(s): 2 WARNING @ Tue, 14 Jul 2020 08:11:59: #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 08:11:59: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:11:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:12:00: 5000000 INFO @ Tue, 14 Jul 2020 08:12:05: 6000000 INFO @ Tue, 14 Jul 2020 08:12:10: 7000000 INFO @ Tue, 14 Jul 2020 08:12:15: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:12:16: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 08:12:21: 9000000 INFO @ Tue, 14 Jul 2020 08:12:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5734949/SRX5734949.10_peaks.xls INFO @ Tue, 14 Jul 2020 08:12:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5734949/SRX5734949.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:12:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5734949/SRX5734949.10_summits.bed INFO @ Tue, 14 Jul 2020 08:12:22: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 08:12:26: 10000000 INFO @ Tue, 14 Jul 2020 08:12:27: #1 tag size is determined as 78 bps INFO @ Tue, 14 Jul 2020 08:12:27: #1 tag size = 78 INFO @ Tue, 14 Jul 2020 08:12:27: #1 total tags in treatment: 10293795 INFO @ Tue, 14 Jul 2020 08:12:27: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:12:27: #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 08:12:28: #1 tags after filtering in treatment: 10293535 INFO @ Tue, 14 Jul 2020 08:12:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 08:12:28: #1 finished! INFO @ Tue, 14 Jul 2020 08:12:28: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:12:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:12:29: #2 number of paired peaks: 3579 INFO @ Tue, 14 Jul 2020 08:12:29: start model_add_line... INFO @ Tue, 14 Jul 2020 08:12:29: start X-correlation... INFO @ Tue, 14 Jul 2020 08:12:29: end of X-cor INFO @ Tue, 14 Jul 2020 08:12:29: #2 finished! INFO @ Tue, 14 Jul 2020 08:12:29: #2 predicted fragment length is 2 bps INFO @ Tue, 14 Jul 2020 08:12:29: #2 alternative fragment length(s) may be 2 bps INFO @ Tue, 14 Jul 2020 08:12:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5734949/SRX5734949.20_model.r WARNING @ Tue, 14 Jul 2020 08:12:29: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:12:29: #2 You may need to consider one of the other alternative d(s): 2 WARNING @ Tue, 14 Jul 2020 08:12:29: #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 08:12:29: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:12:29: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 08:12:45: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:12:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5734949/SRX5734949.20_peaks.xls INFO @ Tue, 14 Jul 2020 08:12:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5734949/SRX5734949.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:12:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5734949/SRX5734949.20_summits.bed INFO @ Tue, 14 Jul 2020 08:12:52: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling