Job ID = 6529174 SRX = SRX026864 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: 00:11:15 46511960 reads; of these: 46511960 (100.00%) were unpaired; of these: 2132580 (4.59%) aligned 0 times 31475289 (67.67%) aligned exactly 1 time 12904091 (27.74%) aligned >1 times 95.41% overall alignment rate Time searching: 00:11:15 Overall time: 00:11:15 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] 20064626 / 44379380 = 0.4521 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 01:45:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX026864/SRX026864.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX026864/SRX026864.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX026864/SRX026864.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX026864/SRX026864.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 01:45:36: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:45:36: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:45:41: 1000000 INFO @ Tue, 30 Jun 2020 01:45:45: 2000000 INFO @ Tue, 30 Jun 2020 01:45:49: 3000000 INFO @ Tue, 30 Jun 2020 01:45:54: 4000000 INFO @ Tue, 30 Jun 2020 01:45:58: 5000000 INFO @ Tue, 30 Jun 2020 01:46:03: 6000000 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 01:46:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX026864/SRX026864.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX026864/SRX026864.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX026864/SRX026864.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX026864/SRX026864.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 01:46:06: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:46:06: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:46:07: 7000000 INFO @ Tue, 30 Jun 2020 01:46:11: 1000000 INFO @ Tue, 30 Jun 2020 01:46:12: 8000000 INFO @ Tue, 30 Jun 2020 01:46:15: 2000000 INFO @ Tue, 30 Jun 2020 01:46:16: 9000000 INFO @ Tue, 30 Jun 2020 01:46:20: 3000000 INFO @ Tue, 30 Jun 2020 01:46:21: 10000000 INFO @ Tue, 30 Jun 2020 01:46:24: 4000000 INFO @ Tue, 30 Jun 2020 01:46:26: 11000000 INFO @ Tue, 30 Jun 2020 01:46:29: 5000000 INFO @ Tue, 30 Jun 2020 01:46:30: 12000000 INFO @ Tue, 30 Jun 2020 01:46:34: 6000000 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 01:46:35: 13000000 INFO @ Tue, 30 Jun 2020 01:46:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX026864/SRX026864.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX026864/SRX026864.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX026864/SRX026864.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX026864/SRX026864.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 01:46:36: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:46:36: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:46:38: 7000000 INFO @ Tue, 30 Jun 2020 01:46:39: 14000000 INFO @ Tue, 30 Jun 2020 01:46:41: 1000000 INFO @ Tue, 30 Jun 2020 01:46:43: 8000000 INFO @ Tue, 30 Jun 2020 01:46:44: 15000000 INFO @ Tue, 30 Jun 2020 01:46:45: 2000000 INFO @ Tue, 30 Jun 2020 01:46:47: 9000000 INFO @ Tue, 30 Jun 2020 01:46:49: 16000000 INFO @ Tue, 30 Jun 2020 01:46:50: 3000000 INFO @ Tue, 30 Jun 2020 01:46:52: 10000000 INFO @ Tue, 30 Jun 2020 01:46:53: 17000000 INFO @ Tue, 30 Jun 2020 01:46:55: 4000000 INFO @ Tue, 30 Jun 2020 01:46:56: 11000000 INFO @ Tue, 30 Jun 2020 01:46:58: 18000000 INFO @ Tue, 30 Jun 2020 01:46:59: 5000000 INFO @ Tue, 30 Jun 2020 01:47:01: 12000000 INFO @ Tue, 30 Jun 2020 01:47:03: 19000000 INFO @ Tue, 30 Jun 2020 01:47:04: 6000000 INFO @ Tue, 30 Jun 2020 01:47:06: 13000000 INFO @ Tue, 30 Jun 2020 01:47:08: 20000000 INFO @ Tue, 30 Jun 2020 01:47:08: 7000000 INFO @ Tue, 30 Jun 2020 01:47:10: 14000000 INFO @ Tue, 30 Jun 2020 01:47:12: 21000000 INFO @ Tue, 30 Jun 2020 01:47:13: 8000000 INFO @ Tue, 30 Jun 2020 01:47:15: 15000000 INFO @ Tue, 30 Jun 2020 01:47:17: 22000000 INFO @ Tue, 30 Jun 2020 01:47:17: 9000000 INFO @ Tue, 30 Jun 2020 01:47:19: 16000000 INFO @ Tue, 30 Jun 2020 01:47:21: 23000000 INFO @ Tue, 30 Jun 2020 01:47:22: 10000000 INFO @ Tue, 30 Jun 2020 01:47:24: 17000000 INFO @ Tue, 30 Jun 2020 01:47:26: 24000000 INFO @ Tue, 30 Jun 2020 01:47:26: 11000000 INFO @ Tue, 30 Jun 2020 01:47:28: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 01:47:28: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 01:47:28: #1 total tags in treatment: 24314754 INFO @ Tue, 30 Jun 2020 01:47:28: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:47:28: #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 01:47:28: 18000000 INFO @ Tue, 30 Jun 2020 01:47:29: #1 tags after filtering in treatment: 24314754 INFO @ Tue, 30 Jun 2020 01:47:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:47:29: #1 finished! INFO @ Tue, 30 Jun 2020 01:47:29: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:47:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:47:30: #2 number of paired peaks: 831 WARNING @ Tue, 30 Jun 2020 01:47:30: Fewer paired peaks (831) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 831 pairs to build model! INFO @ Tue, 30 Jun 2020 01:47:30: start model_add_line... INFO @ Tue, 30 Jun 2020 01:47:30: start X-correlation... INFO @ Tue, 30 Jun 2020 01:47:30: end of X-cor INFO @ Tue, 30 Jun 2020 01:47:30: #2 finished! INFO @ Tue, 30 Jun 2020 01:47:30: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 01:47:30: #2 alternative fragment length(s) may be 2,33 bps INFO @ Tue, 30 Jun 2020 01:47:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX026864/SRX026864.05_model.r WARNING @ Tue, 30 Jun 2020 01:47:30: #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 01:47:30: #2 You may need to consider one of the other alternative d(s): 2,33 WARNING @ Tue, 30 Jun 2020 01:47:30: #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 01:47:30: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:47:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:47:31: 12000000 INFO @ Tue, 30 Jun 2020 01:47:33: 19000000 INFO @ Tue, 30 Jun 2020 01:47:36: 13000000 INFO @ Tue, 30 Jun 2020 01:47:38: 20000000 INFO @ Tue, 30 Jun 2020 01:47:40: 14000000 INFO @ Tue, 30 Jun 2020 01:47:42: 21000000 INFO @ Tue, 30 Jun 2020 01:47:45: 15000000 INFO @ Tue, 30 Jun 2020 01:47:47: 22000000 INFO @ Tue, 30 Jun 2020 01:47:50: 16000000 INFO @ Tue, 30 Jun 2020 01:47:51: 23000000 INFO @ Tue, 30 Jun 2020 01:47:54: 17000000 INFO @ Tue, 30 Jun 2020 01:47:56: 24000000 INFO @ Tue, 30 Jun 2020 01:47:58: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 01:47:58: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 01:47:58: #1 total tags in treatment: 24314754 INFO @ Tue, 30 Jun 2020 01:47:58: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:47:58: #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 01:47:58: #1 tags after filtering in treatment: 24314754 INFO @ Tue, 30 Jun 2020 01:47:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:47:58: #1 finished! INFO @ Tue, 30 Jun 2020 01:47:58: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:47:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:47:59: 18000000 INFO @ Tue, 30 Jun 2020 01:48:00: #2 number of paired peaks: 831 WARNING @ Tue, 30 Jun 2020 01:48:00: Fewer paired peaks (831) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 831 pairs to build model! INFO @ Tue, 30 Jun 2020 01:48:00: start model_add_line... INFO @ Tue, 30 Jun 2020 01:48:00: start X-correlation... INFO @ Tue, 30 Jun 2020 01:48:00: end of X-cor INFO @ Tue, 30 Jun 2020 01:48:00: #2 finished! INFO @ Tue, 30 Jun 2020 01:48:00: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 01:48:00: #2 alternative fragment length(s) may be 2,33 bps INFO @ Tue, 30 Jun 2020 01:48:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX026864/SRX026864.10_model.r WARNING @ Tue, 30 Jun 2020 01:48:00: #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 01:48:00: #2 You may need to consider one of the other alternative d(s): 2,33 WARNING @ Tue, 30 Jun 2020 01:48:00: #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 01:48:00: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:48:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:48:04: 19000000 INFO @ Tue, 30 Jun 2020 01:48:09: 20000000 INFO @ Tue, 30 Jun 2020 01:48:09: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 01:48:13: 21000000 INFO @ Tue, 30 Jun 2020 01:48:18: 22000000 INFO @ Tue, 30 Jun 2020 01:48:22: 23000000 INFO @ Tue, 30 Jun 2020 01:48:27: 24000000 INFO @ Tue, 30 Jun 2020 01:48:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX026864/SRX026864.05_peaks.xls INFO @ Tue, 30 Jun 2020 01:48:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX026864/SRX026864.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:48:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX026864/SRX026864.05_summits.bed INFO @ Tue, 30 Jun 2020 01:48:27: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:48:29: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 01:48:29: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 01:48:29: #1 total tags in treatment: 24314754 INFO @ Tue, 30 Jun 2020 01:48:29: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:48:29: #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 01:48:29: #1 tags after filtering in treatment: 24314754 INFO @ Tue, 30 Jun 2020 01:48:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:48:29: #1 finished! INFO @ Tue, 30 Jun 2020 01:48:29: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:48:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:48:31: #2 number of paired peaks: 831 WARNING @ Tue, 30 Jun 2020 01:48:31: Fewer paired peaks (831) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 831 pairs to build model! INFO @ Tue, 30 Jun 2020 01:48:31: start model_add_line... INFO @ Tue, 30 Jun 2020 01:48:31: start X-correlation... INFO @ Tue, 30 Jun 2020 01:48:31: end of X-cor INFO @ Tue, 30 Jun 2020 01:48:31: #2 finished! INFO @ Tue, 30 Jun 2020 01:48:31: #2 predicted fragment length is 2 bps INFO @ Tue, 30 Jun 2020 01:48:31: #2 alternative fragment length(s) may be 2,33 bps INFO @ Tue, 30 Jun 2020 01:48:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX026864/SRX026864.20_model.r WARNING @ Tue, 30 Jun 2020 01:48:31: #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 01:48:31: #2 You may need to consider one of the other alternative d(s): 2,33 WARNING @ Tue, 30 Jun 2020 01:48:31: #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 01:48:31: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:48:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:48:39: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:48:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX026864/SRX026864.10_peaks.xls INFO @ Tue, 30 Jun 2020 01:48:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX026864/SRX026864.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:48:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX026864/SRX026864.10_summits.bed INFO @ Tue, 30 Jun 2020 01:48:57: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 01:49:10: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:49:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX026864/SRX026864.20_peaks.xls INFO @ Tue, 30 Jun 2020 01:49:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX026864/SRX026864.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:49:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX026864/SRX026864.20_summits.bed INFO @ Tue, 30 Jun 2020 01:49:28: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling