Job ID = 6454502 SRX = SRX2165286 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:09:09 prefetch.2.10.7: 1) Downloading 'SRR4244801'... 2020-06-21T09:09:09 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:14:00 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:14:00 prefetch.2.10.7: 1) 'SRR4244801' was downloaded successfully Read 21199238 spots for SRR4244801/SRR4244801.sra Written 21199238 spots for SRR4244801/SRR4244801.sra 2020-06-21T09:15:29 prefetch.2.10.7: 1) Downloading 'SRR4244802'... 2020-06-21T09:15:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:19:44 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:19:44 prefetch.2.10.7: 1) 'SRR4244802' was downloaded successfully Read 17863221 spots for SRR4244802/SRR4244802.sra Written 17863221 spots for SRR4244802/SRR4244802.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: 00:13:02 39062459 reads; of these: 39062459 (100.00%) were unpaired; of these: 6154382 (15.76%) aligned 0 times 24111168 (61.72%) aligned exactly 1 time 8796909 (22.52%) aligned >1 times 84.24% overall alignment rate Time searching: 00:13:02 Overall time: 00:13:02 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 16 files... [bam_rmdupse_core] 16338811 / 32908077 = 0.4965 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 18:43:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2165286/SRX2165286.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2165286/SRX2165286.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2165286/SRX2165286.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2165286/SRX2165286.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 18:43:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:43:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:43:59: 1000000 INFO @ Sun, 21 Jun 2020 18:44:04: 2000000 INFO @ Sun, 21 Jun 2020 18:44:10: 3000000 INFO @ Sun, 21 Jun 2020 18:44:15: 4000000 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 18:44:21: 5000000 INFO @ Sun, 21 Jun 2020 18:44:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2165286/SRX2165286.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2165286/SRX2165286.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2165286/SRX2165286.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2165286/SRX2165286.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 18:44:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:44:22: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:44:27: 6000000 INFO @ Sun, 21 Jun 2020 18:44:29: 1000000 INFO @ Sun, 21 Jun 2020 18:44:33: 7000000 INFO @ Sun, 21 Jun 2020 18:44:35: 2000000 INFO @ Sun, 21 Jun 2020 18:44:38: 8000000 INFO @ Sun, 21 Jun 2020 18:44:41: 3000000 INFO @ Sun, 21 Jun 2020 18:44:44: 9000000 INFO @ Sun, 21 Jun 2020 18:44:47: 4000000 INFO @ Sun, 21 Jun 2020 18:44:50: 10000000 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 18:44:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2165286/SRX2165286.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2165286/SRX2165286.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2165286/SRX2165286.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2165286/SRX2165286.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 18:44:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:44:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:44:54: 5000000 INFO @ Sun, 21 Jun 2020 18:44:56: 11000000 INFO @ Sun, 21 Jun 2020 18:44:59: 1000000 INFO @ Sun, 21 Jun 2020 18:45:01: 6000000 INFO @ Sun, 21 Jun 2020 18:45:02: 12000000 INFO @ Sun, 21 Jun 2020 18:45:05: 2000000 INFO @ Sun, 21 Jun 2020 18:45:08: 7000000 INFO @ Sun, 21 Jun 2020 18:45:08: 13000000 INFO @ Sun, 21 Jun 2020 18:45:11: 3000000 INFO @ Sun, 21 Jun 2020 18:45:15: 8000000 INFO @ Sun, 21 Jun 2020 18:45:15: 14000000 INFO @ Sun, 21 Jun 2020 18:45:17: 4000000 INFO @ Sun, 21 Jun 2020 18:45:22: 15000000 INFO @ Sun, 21 Jun 2020 18:45:23: 9000000 INFO @ Sun, 21 Jun 2020 18:45:24: 5000000 INFO @ Sun, 21 Jun 2020 18:45:28: 16000000 INFO @ Sun, 21 Jun 2020 18:45:30: 6000000 INFO @ Sun, 21 Jun 2020 18:45:31: 10000000 INFO @ Sun, 21 Jun 2020 18:45:32: #1 tag size is determined as 67 bps INFO @ Sun, 21 Jun 2020 18:45:32: #1 tag size = 67 INFO @ Sun, 21 Jun 2020 18:45:32: #1 total tags in treatment: 16569266 INFO @ Sun, 21 Jun 2020 18:45:32: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:45:32: #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 18:45:33: #1 tags after filtering in treatment: 16569258 INFO @ Sun, 21 Jun 2020 18:45:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:45:33: #1 finished! INFO @ Sun, 21 Jun 2020 18:45:33: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:45:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:45:34: #2 number of paired peaks: 948 WARNING @ Sun, 21 Jun 2020 18:45:34: Fewer paired peaks (948) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 948 pairs to build model! INFO @ Sun, 21 Jun 2020 18:45:34: start model_add_line... INFO @ Sun, 21 Jun 2020 18:45:34: start X-correlation... INFO @ Sun, 21 Jun 2020 18:45:34: end of X-cor INFO @ Sun, 21 Jun 2020 18:45:34: #2 finished! INFO @ Sun, 21 Jun 2020 18:45:34: #2 predicted fragment length is 67 bps INFO @ Sun, 21 Jun 2020 18:45:34: #2 alternative fragment length(s) may be 3,67 bps INFO @ Sun, 21 Jun 2020 18:45:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2165286/SRX2165286.05_model.r WARNING @ Sun, 21 Jun 2020 18:45:34: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:45:34: #2 You may need to consider one of the other alternative d(s): 3,67 WARNING @ Sun, 21 Jun 2020 18:45:34: #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 18:45:34: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:45:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:45:36: 7000000 INFO @ Sun, 21 Jun 2020 18:45:38: 11000000 INFO @ Sun, 21 Jun 2020 18:45:41: 8000000 INFO @ Sun, 21 Jun 2020 18:45:46: 12000000 INFO @ Sun, 21 Jun 2020 18:45:47: 9000000 INFO @ Sun, 21 Jun 2020 18:45:53: 10000000 INFO @ Sun, 21 Jun 2020 18:45:54: 13000000 INFO @ Sun, 21 Jun 2020 18:45:59: 11000000 INFO @ Sun, 21 Jun 2020 18:46:02: 14000000 INFO @ Sun, 21 Jun 2020 18:46:05: 12000000 INFO @ Sun, 21 Jun 2020 18:46:05: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:46:10: 15000000 INFO @ Sun, 21 Jun 2020 18:46:12: 13000000 INFO @ Sun, 21 Jun 2020 18:46:17: 16000000 INFO @ Sun, 21 Jun 2020 18:46:19: 14000000 INFO @ Sun, 21 Jun 2020 18:46:22: #1 tag size is determined as 67 bps INFO @ Sun, 21 Jun 2020 18:46:22: #1 tag size = 67 INFO @ Sun, 21 Jun 2020 18:46:22: #1 total tags in treatment: 16569266 INFO @ Sun, 21 Jun 2020 18:46:22: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:46:22: #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 18:46:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2165286/SRX2165286.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:46:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2165286/SRX2165286.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:46:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2165286/SRX2165286.05_summits.bed INFO @ Sun, 21 Jun 2020 18:46:23: Done! INFO @ Sun, 21 Jun 2020 18:46:23: #1 tags after filtering in treatment: 16569258 INFO @ Sun, 21 Jun 2020 18:46:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:46:23: #1 finished! INFO @ Sun, 21 Jun 2020 18:46:23: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:46:23: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (800 chroms): 2 millis pass2 - checking and writing primary data (3901 records, 4 fields): 49 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:46:24: #2 number of paired peaks: 948 WARNING @ Sun, 21 Jun 2020 18:46:24: Fewer paired peaks (948) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 948 pairs to build model! INFO @ Sun, 21 Jun 2020 18:46:24: start model_add_line... INFO @ Sun, 21 Jun 2020 18:46:24: start X-correlation... INFO @ Sun, 21 Jun 2020 18:46:24: end of X-cor INFO @ Sun, 21 Jun 2020 18:46:24: #2 finished! INFO @ Sun, 21 Jun 2020 18:46:24: #2 predicted fragment length is 67 bps INFO @ Sun, 21 Jun 2020 18:46:24: #2 alternative fragment length(s) may be 3,67 bps INFO @ Sun, 21 Jun 2020 18:46:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2165286/SRX2165286.10_model.r WARNING @ Sun, 21 Jun 2020 18:46:24: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:46:24: #2 You may need to consider one of the other alternative d(s): 3,67 WARNING @ Sun, 21 Jun 2020 18:46:24: #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 18:46:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:46:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:46:26: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:46:33: 16000000 INFO @ Sun, 21 Jun 2020 18:46:37: #1 tag size is determined as 67 bps INFO @ Sun, 21 Jun 2020 18:46:37: #1 tag size = 67 INFO @ Sun, 21 Jun 2020 18:46:37: #1 total tags in treatment: 16569266 INFO @ Sun, 21 Jun 2020 18:46:37: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:46:37: #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 18:46:38: #1 tags after filtering in treatment: 16569258 INFO @ Sun, 21 Jun 2020 18:46:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:46:38: #1 finished! INFO @ Sun, 21 Jun 2020 18:46:38: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:46:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:46:39: #2 number of paired peaks: 948 WARNING @ Sun, 21 Jun 2020 18:46:39: Fewer paired peaks (948) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 948 pairs to build model! INFO @ Sun, 21 Jun 2020 18:46:39: start model_add_line... INFO @ Sun, 21 Jun 2020 18:46:39: start X-correlation... INFO @ Sun, 21 Jun 2020 18:46:39: end of X-cor INFO @ Sun, 21 Jun 2020 18:46:39: #2 finished! INFO @ Sun, 21 Jun 2020 18:46:39: #2 predicted fragment length is 67 bps INFO @ Sun, 21 Jun 2020 18:46:39: #2 alternative fragment length(s) may be 3,67 bps INFO @ Sun, 21 Jun 2020 18:46:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2165286/SRX2165286.20_model.r WARNING @ Sun, 21 Jun 2020 18:46:39: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:46:39: #2 You may need to consider one of the other alternative d(s): 3,67 WARNING @ Sun, 21 Jun 2020 18:46:39: #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 18:46:39: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:46:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:46:55: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:47:11: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:47:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2165286/SRX2165286.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:47:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2165286/SRX2165286.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:47:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2165286/SRX2165286.10_summits.bed INFO @ Sun, 21 Jun 2020 18:47:12: Done! pass1 - making usageList (651 chroms): 2 millis pass2 - checking and writing primary data (2537 records, 4 fields): 37 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:47:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2165286/SRX2165286.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:47:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2165286/SRX2165286.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:47:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2165286/SRX2165286.20_summits.bed INFO @ Sun, 21 Jun 2020 18:47:27: Done! pass1 - making usageList (530 chroms): 2 millis pass2 - checking and writing primary data (1653 records, 4 fields): 30 millis CompletedMACS2peakCalling