Job ID = 6453287 SRX = SRX110798 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:12:03 prefetch.2.10.7: 1) Downloading 'SRR388380'... 2020-06-21T08:12:03 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:15:38 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:15:38 prefetch.2.10.7: 'SRR388380' is valid 2020-06-21T08:15:38 prefetch.2.10.7: 1) 'SRR388380' was downloaded successfully Read 31543517 spots for SRR388380/SRR388380.sra Written 31543517 spots for SRR388380/SRR388380.sra 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: 00:09:29 31543517 reads; of these: 31543517 (100.00%) were unpaired; of these: 2478432 (7.86%) aligned 0 times 16305381 (51.69%) aligned exactly 1 time 12759704 (40.45%) aligned >1 times 92.14% overall alignment rate Time searching: 00:09:29 Overall time: 00:09:29 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] 5767698 / 29065085 = 0.1984 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 @ Sun, 21 Jun 2020 17:30:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX110798/SRX110798.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX110798/SRX110798.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX110798/SRX110798.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX110798/SRX110798.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 @ Sun, 21 Jun 2020 17:30:56: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:30:56: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:31:01: 1000000 INFO @ Sun, 21 Jun 2020 17:31:05: 2000000 INFO @ Sun, 21 Jun 2020 17:31:10: 3000000 INFO @ Sun, 21 Jun 2020 17:31:15: 4000000 INFO @ Sun, 21 Jun 2020 17:31:20: 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 @ Sun, 21 Jun 2020 17:31:24: 6000000 INFO @ Sun, 21 Jun 2020 17:31:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX110798/SRX110798.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX110798/SRX110798.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX110798/SRX110798.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX110798/SRX110798.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 @ Sun, 21 Jun 2020 17:31:26: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:31:26: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:31:29: 7000000 INFO @ Sun, 21 Jun 2020 17:31:31: 1000000 INFO @ Sun, 21 Jun 2020 17:31:34: 8000000 INFO @ Sun, 21 Jun 2020 17:31:36: 2000000 INFO @ Sun, 21 Jun 2020 17:31:39: 9000000 INFO @ Sun, 21 Jun 2020 17:31:41: 3000000 INFO @ Sun, 21 Jun 2020 17:31:44: 10000000 INFO @ Sun, 21 Jun 2020 17:31:46: 4000000 INFO @ Sun, 21 Jun 2020 17:31:49: 11000000 INFO @ Sun, 21 Jun 2020 17:31:51: 5000000 INFO @ Sun, 21 Jun 2020 17:31:54: 12000000 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 @ Sun, 21 Jun 2020 17:31:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX110798/SRX110798.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX110798/SRX110798.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX110798/SRX110798.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX110798/SRX110798.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 @ Sun, 21 Jun 2020 17:31:56: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:31:56: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:31:56: 6000000 INFO @ Sun, 21 Jun 2020 17:31:59: 13000000 INFO @ Sun, 21 Jun 2020 17:32:01: 1000000 INFO @ Sun, 21 Jun 2020 17:32:02: 7000000 INFO @ Sun, 21 Jun 2020 17:32:04: 14000000 INFO @ Sun, 21 Jun 2020 17:32:06: 2000000 INFO @ Sun, 21 Jun 2020 17:32:07: 8000000 INFO @ Sun, 21 Jun 2020 17:32:09: 15000000 INFO @ Sun, 21 Jun 2020 17:32:11: 3000000 INFO @ Sun, 21 Jun 2020 17:32:12: 9000000 INFO @ Sun, 21 Jun 2020 17:32:13: 16000000 INFO @ Sun, 21 Jun 2020 17:32:16: 4000000 INFO @ Sun, 21 Jun 2020 17:32:17: 10000000 INFO @ Sun, 21 Jun 2020 17:32:18: 17000000 INFO @ Sun, 21 Jun 2020 17:32:21: 5000000 INFO @ Sun, 21 Jun 2020 17:32:21: 11000000 INFO @ Sun, 21 Jun 2020 17:32:23: 18000000 INFO @ Sun, 21 Jun 2020 17:32:26: 6000000 INFO @ Sun, 21 Jun 2020 17:32:27: 12000000 INFO @ Sun, 21 Jun 2020 17:32:28: 19000000 INFO @ Sun, 21 Jun 2020 17:32:31: 7000000 INFO @ Sun, 21 Jun 2020 17:32:32: 13000000 INFO @ Sun, 21 Jun 2020 17:32:33: 20000000 INFO @ Sun, 21 Jun 2020 17:32:36: 8000000 INFO @ Sun, 21 Jun 2020 17:32:37: 14000000 INFO @ Sun, 21 Jun 2020 17:32:38: 21000000 INFO @ Sun, 21 Jun 2020 17:32:41: 9000000 INFO @ Sun, 21 Jun 2020 17:32:41: 15000000 INFO @ Sun, 21 Jun 2020 17:32:43: 22000000 INFO @ Sun, 21 Jun 2020 17:32:46: 10000000 INFO @ Sun, 21 Jun 2020 17:32:46: 16000000 INFO @ Sun, 21 Jun 2020 17:32:48: 23000000 INFO @ Sun, 21 Jun 2020 17:32:50: #1 tag size is determined as 18 bps INFO @ Sun, 21 Jun 2020 17:32:50: #1 tag size = 18 INFO @ Sun, 21 Jun 2020 17:32:50: #1 total tags in treatment: 23297387 INFO @ Sun, 21 Jun 2020 17:32:50: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:32:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 17:32:50: #1 tags after filtering in treatment: 23297387 INFO @ Sun, 21 Jun 2020 17:32:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:32:50: #1 finished! INFO @ Sun, 21 Jun 2020 17:32:50: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:32:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:32:51: 11000000 INFO @ Sun, 21 Jun 2020 17:32:51: 17000000 INFO @ Sun, 21 Jun 2020 17:32:52: #2 number of paired peaks: 128 WARNING @ Sun, 21 Jun 2020 17:32:52: Fewer paired peaks (128) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 128 pairs to build model! INFO @ Sun, 21 Jun 2020 17:32:52: start model_add_line... INFO @ Sun, 21 Jun 2020 17:32:52: start X-correlation... INFO @ Sun, 21 Jun 2020 17:32:52: end of X-cor INFO @ Sun, 21 Jun 2020 17:32:52: #2 finished! INFO @ Sun, 21 Jun 2020 17:32:52: #2 predicted fragment length is 3 bps INFO @ Sun, 21 Jun 2020 17:32:52: #2 alternative fragment length(s) may be 3 bps INFO @ Sun, 21 Jun 2020 17:32:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX110798/SRX110798.05_model.r WARNING @ Sun, 21 Jun 2020 17:32:52: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:32:52: #2 You may need to consider one of the other alternative d(s): 3 WARNING @ Sun, 21 Jun 2020 17:32:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 17:32:52: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:32:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:32:56: 18000000 INFO @ Sun, 21 Jun 2020 17:32:56: 12000000 INFO @ Sun, 21 Jun 2020 17:33:01: 19000000 INFO @ Sun, 21 Jun 2020 17:33:01: 13000000 INFO @ Sun, 21 Jun 2020 17:33:06: 14000000 INFO @ Sun, 21 Jun 2020 17:33:06: 20000000 INFO @ Sun, 21 Jun 2020 17:33:11: 15000000 INFO @ Sun, 21 Jun 2020 17:33:11: 21000000 INFO @ Sun, 21 Jun 2020 17:33:16: 16000000 INFO @ Sun, 21 Jun 2020 17:33:16: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:33:21: 17000000 INFO @ Sun, 21 Jun 2020 17:33:21: 23000000 INFO @ Sun, 21 Jun 2020 17:33:23: #1 tag size is determined as 18 bps INFO @ Sun, 21 Jun 2020 17:33:23: #1 tag size = 18 INFO @ Sun, 21 Jun 2020 17:33:23: #1 total tags in treatment: 23297387 INFO @ Sun, 21 Jun 2020 17:33:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:33:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 17:33:23: #1 tags after filtering in treatment: 23297387 INFO @ Sun, 21 Jun 2020 17:33:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:33:23: #1 finished! INFO @ Sun, 21 Jun 2020 17:33:23: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:33:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:33:25: #2 number of paired peaks: 128 WARNING @ Sun, 21 Jun 2020 17:33:25: Fewer paired peaks (128) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 128 pairs to build model! INFO @ Sun, 21 Jun 2020 17:33:25: start model_add_line... INFO @ Sun, 21 Jun 2020 17:33:25: start X-correlation... INFO @ Sun, 21 Jun 2020 17:33:25: end of X-cor INFO @ Sun, 21 Jun 2020 17:33:25: #2 finished! INFO @ Sun, 21 Jun 2020 17:33:25: #2 predicted fragment length is 3 bps INFO @ Sun, 21 Jun 2020 17:33:25: #2 alternative fragment length(s) may be 3 bps INFO @ Sun, 21 Jun 2020 17:33:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX110798/SRX110798.10_model.r WARNING @ Sun, 21 Jun 2020 17:33:25: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:33:25: #2 You may need to consider one of the other alternative d(s): 3 WARNING @ Sun, 21 Jun 2020 17:33:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 17:33:25: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:33:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:33:26: 18000000 INFO @ Sun, 21 Jun 2020 17:33:28: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:33:31: 19000000 INFO @ Sun, 21 Jun 2020 17:33:36: 20000000 INFO @ Sun, 21 Jun 2020 17:33:40: 21000000 INFO @ Sun, 21 Jun 2020 17:33:45: 22000000 INFO @ Sun, 21 Jun 2020 17:33:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX110798/SRX110798.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:33:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX110798/SRX110798.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:33:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX110798/SRX110798.05_summits.bed INFO @ Sun, 21 Jun 2020 17:33:46: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:33:50: 23000000 INFO @ Sun, 21 Jun 2020 17:33:52: #1 tag size is determined as 18 bps INFO @ Sun, 21 Jun 2020 17:33:52: #1 tag size = 18 INFO @ Sun, 21 Jun 2020 17:33:52: #1 total tags in treatment: 23297387 INFO @ Sun, 21 Jun 2020 17:33:52: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:33:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 17:33:52: #1 tags after filtering in treatment: 23297387 INFO @ Sun, 21 Jun 2020 17:33:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:33:52: #1 finished! INFO @ Sun, 21 Jun 2020 17:33:52: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:33:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:33:54: #2 number of paired peaks: 128 WARNING @ Sun, 21 Jun 2020 17:33:54: Fewer paired peaks (128) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 128 pairs to build model! INFO @ Sun, 21 Jun 2020 17:33:54: start model_add_line... INFO @ Sun, 21 Jun 2020 17:33:54: start X-correlation... INFO @ Sun, 21 Jun 2020 17:33:54: end of X-cor INFO @ Sun, 21 Jun 2020 17:33:54: #2 finished! INFO @ Sun, 21 Jun 2020 17:33:54: #2 predicted fragment length is 3 bps INFO @ Sun, 21 Jun 2020 17:33:54: #2 alternative fragment length(s) may be 3 bps INFO @ Sun, 21 Jun 2020 17:33:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX110798/SRX110798.20_model.r WARNING @ Sun, 21 Jun 2020 17:33:54: #2 Since the d (3) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:33:54: #2 You may need to consider one of the other alternative d(s): 3 WARNING @ Sun, 21 Jun 2020 17:33:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 17:33:54: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:33:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:34:01: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:34:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX110798/SRX110798.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:34:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX110798/SRX110798.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:34:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX110798/SRX110798.10_summits.bed INFO @ Sun, 21 Jun 2020 17:34:20: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:34:30: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:34:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX110798/SRX110798.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:34:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX110798/SRX110798.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:34:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX110798/SRX110798.20_summits.bed INFO @ Sun, 21 Jun 2020 17:34:48: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling