Job ID = 6529525 SRX = SRX287929 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: 00:06:45 22382823 reads; of these: 22382823 (100.00%) were unpaired; of these: 1401379 (6.26%) aligned 0 times 14498803 (64.78%) aligned exactly 1 time 6482641 (28.96%) aligned >1 times 93.74% overall alignment rate Time searching: 00:06:45 Overall time: 00:06:45 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] 5662045 / 20981444 = 0.2699 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 02:24:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287929/SRX287929.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287929/SRX287929.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287929/SRX287929.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287929/SRX287929.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 02:24:35: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:24:35: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:24:42: 1000000 INFO @ Tue, 30 Jun 2020 02:24:49: 2000000 INFO @ Tue, 30 Jun 2020 02:24:57: 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 02:25:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287929/SRX287929.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287929/SRX287929.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287929/SRX287929.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287929/SRX287929.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 02:25:04: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:25:04: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:25:04: 4000000 INFO @ Tue, 30 Jun 2020 02:25:12: 1000000 INFO @ Tue, 30 Jun 2020 02:25:12: 5000000 INFO @ Tue, 30 Jun 2020 02:25:20: 2000000 INFO @ Tue, 30 Jun 2020 02:25:20: 6000000 INFO @ Tue, 30 Jun 2020 02:25:28: 3000000 INFO @ Tue, 30 Jun 2020 02:25:28: 7000000 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 02:25:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287929/SRX287929.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287929/SRX287929.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287929/SRX287929.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287929/SRX287929.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 02:25:35: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:25:35: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:25:35: 4000000 INFO @ Tue, 30 Jun 2020 02:25:35: 8000000 INFO @ Tue, 30 Jun 2020 02:25:43: 1000000 INFO @ Tue, 30 Jun 2020 02:25:43: 5000000 INFO @ Tue, 30 Jun 2020 02:25:43: 9000000 INFO @ Tue, 30 Jun 2020 02:25:50: 2000000 INFO @ Tue, 30 Jun 2020 02:25:51: 10000000 INFO @ Tue, 30 Jun 2020 02:25:51: 6000000 INFO @ Tue, 30 Jun 2020 02:25:58: 3000000 INFO @ Tue, 30 Jun 2020 02:25:59: 11000000 INFO @ Tue, 30 Jun 2020 02:25:59: 7000000 INFO @ Tue, 30 Jun 2020 02:26:06: 4000000 INFO @ Tue, 30 Jun 2020 02:26:06: 12000000 INFO @ Tue, 30 Jun 2020 02:26:07: 8000000 INFO @ Tue, 30 Jun 2020 02:26:14: 5000000 INFO @ Tue, 30 Jun 2020 02:26:15: 13000000 INFO @ Tue, 30 Jun 2020 02:26:15: 9000000 INFO @ Tue, 30 Jun 2020 02:26:21: 6000000 INFO @ Tue, 30 Jun 2020 02:26:22: 14000000 INFO @ Tue, 30 Jun 2020 02:26:23: 10000000 INFO @ Tue, 30 Jun 2020 02:26:29: 7000000 INFO @ Tue, 30 Jun 2020 02:26:30: 15000000 INFO @ Tue, 30 Jun 2020 02:26:31: 11000000 INFO @ Tue, 30 Jun 2020 02:26:33: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:26:33: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:26:33: #1 total tags in treatment: 15319399 INFO @ Tue, 30 Jun 2020 02:26:33: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:26:33: #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 02:26:34: #1 tags after filtering in treatment: 15319399 INFO @ Tue, 30 Jun 2020 02:26:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:26:34: #1 finished! INFO @ Tue, 30 Jun 2020 02:26:34: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:26:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:26:35: #2 number of paired peaks: 810 WARNING @ Tue, 30 Jun 2020 02:26:35: Fewer paired peaks (810) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 810 pairs to build model! INFO @ Tue, 30 Jun 2020 02:26:35: start model_add_line... INFO @ Tue, 30 Jun 2020 02:26:35: start X-correlation... INFO @ Tue, 30 Jun 2020 02:26:35: end of X-cor INFO @ Tue, 30 Jun 2020 02:26:35: #2 finished! INFO @ Tue, 30 Jun 2020 02:26:35: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 02:26:35: #2 alternative fragment length(s) may be 2,18,554 bps INFO @ Tue, 30 Jun 2020 02:26:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287929/SRX287929.05_model.r WARNING @ Tue, 30 Jun 2020 02:26:35: #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, 30 Jun 2020 02:26:35: #2 You may need to consider one of the other alternative d(s): 2,18,554 WARNING @ Tue, 30 Jun 2020 02:26:35: #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 02:26:35: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:26:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:26:37: 8000000 INFO @ Tue, 30 Jun 2020 02:26:39: 12000000 INFO @ Tue, 30 Jun 2020 02:26:44: 9000000 INFO @ Tue, 30 Jun 2020 02:26:47: 13000000 INFO @ Tue, 30 Jun 2020 02:26:51: 10000000 INFO @ Tue, 30 Jun 2020 02:26:55: 14000000 INFO @ Tue, 30 Jun 2020 02:26:57: 11000000 INFO @ Tue, 30 Jun 2020 02:27:00: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:27:03: 15000000 INFO @ Tue, 30 Jun 2020 02:27:04: 12000000 INFO @ Tue, 30 Jun 2020 02:27:06: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:27:06: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:27:06: #1 total tags in treatment: 15319399 INFO @ Tue, 30 Jun 2020 02:27:06: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:27:06: #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 02:27:07: #1 tags after filtering in treatment: 15319399 INFO @ Tue, 30 Jun 2020 02:27:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:27:07: #1 finished! INFO @ Tue, 30 Jun 2020 02:27:07: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:27:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:27:08: #2 number of paired peaks: 810 WARNING @ Tue, 30 Jun 2020 02:27:08: Fewer paired peaks (810) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 810 pairs to build model! INFO @ Tue, 30 Jun 2020 02:27:08: start model_add_line... INFO @ Tue, 30 Jun 2020 02:27:08: start X-correlation... INFO @ Tue, 30 Jun 2020 02:27:08: end of X-cor INFO @ Tue, 30 Jun 2020 02:27:08: #2 finished! INFO @ Tue, 30 Jun 2020 02:27:08: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 02:27:08: #2 alternative fragment length(s) may be 2,18,554 bps INFO @ Tue, 30 Jun 2020 02:27:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287929/SRX287929.10_model.r WARNING @ Tue, 30 Jun 2020 02:27:08: #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, 30 Jun 2020 02:27:08: #2 You may need to consider one of the other alternative d(s): 2,18,554 WARNING @ Tue, 30 Jun 2020 02:27:08: #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 02:27:08: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:27:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:27:12: 13000000 INFO @ Tue, 30 Jun 2020 02:27:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287929/SRX287929.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:27:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287929/SRX287929.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:27:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287929/SRX287929.05_summits.bed INFO @ Tue, 30 Jun 2020 02:27:13: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:27:18: 14000000 INFO @ Tue, 30 Jun 2020 02:27:25: 15000000 INFO @ Tue, 30 Jun 2020 02:27:27: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:27:27: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:27:27: #1 total tags in treatment: 15319399 INFO @ Tue, 30 Jun 2020 02:27:27: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:27:27: #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 02:27:28: #1 tags after filtering in treatment: 15319399 INFO @ Tue, 30 Jun 2020 02:27:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:27:28: #1 finished! INFO @ Tue, 30 Jun 2020 02:27:28: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:27:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:27:29: #2 number of paired peaks: 810 WARNING @ Tue, 30 Jun 2020 02:27:29: Fewer paired peaks (810) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 810 pairs to build model! INFO @ Tue, 30 Jun 2020 02:27:29: start model_add_line... INFO @ Tue, 30 Jun 2020 02:27:29: start X-correlation... INFO @ Tue, 30 Jun 2020 02:27:29: end of X-cor INFO @ Tue, 30 Jun 2020 02:27:29: #2 finished! INFO @ Tue, 30 Jun 2020 02:27:29: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 02:27:29: #2 alternative fragment length(s) may be 2,18,554 bps INFO @ Tue, 30 Jun 2020 02:27:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287929/SRX287929.20_model.r WARNING @ Tue, 30 Jun 2020 02:27:29: #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, 30 Jun 2020 02:27:29: #2 You may need to consider one of the other alternative d(s): 2,18,554 WARNING @ Tue, 30 Jun 2020 02:27:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:27:29: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:27:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:27:33: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:27:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287929/SRX287929.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:27:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287929/SRX287929.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:27:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287929/SRX287929.10_summits.bed INFO @ Tue, 30 Jun 2020 02:27:46: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:27:55: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:28:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287929/SRX287929.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:28:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287929/SRX287929.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:28:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287929/SRX287929.20_summits.bed INFO @ Tue, 30 Jun 2020 02:28:07: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling