Job ID = 6527491 SRX = SRX032119 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T12:22:50 prefetch.2.10.7: 1) Downloading 'SRR073941'... 2020-06-29T12:22:50 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:25:27 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:25:28 prefetch.2.10.7: 'SRR073941' is valid 2020-06-29T12:25:28 prefetch.2.10.7: 1) 'SRR073941' was downloaded successfully Read 24896839 spots for SRR073941/SRR073941.sra Written 24896839 spots for SRR073941/SRR073941.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: 00:11:04 24896839 reads; of these: 24896839 (100.00%) were unpaired; of these: 193004 (0.78%) aligned 0 times 15868158 (63.74%) aligned exactly 1 time 8835677 (35.49%) aligned >1 times 99.22% overall alignment rate Time searching: 00:11:04 Overall time: 00:11:04 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 5687111 / 24703835 = 0.2302 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 @ Mon, 29 Jun 2020 21:49:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX032119/SRX032119.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX032119/SRX032119.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX032119/SRX032119.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX032119/SRX032119.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 @ Mon, 29 Jun 2020 21:49:15: #1 read tag files... INFO @ Mon, 29 Jun 2020 21:49:15: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 21:49:22: 1000000 INFO @ Mon, 29 Jun 2020 21:49:29: 2000000 INFO @ Mon, 29 Jun 2020 21:49:35: 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 @ Mon, 29 Jun 2020 21:49:42: 4000000 INFO @ Mon, 29 Jun 2020 21:49:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX032119/SRX032119.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX032119/SRX032119.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX032119/SRX032119.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX032119/SRX032119.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 @ Mon, 29 Jun 2020 21:49:45: #1 read tag files... INFO @ Mon, 29 Jun 2020 21:49:45: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 21:49:49: 5000000 INFO @ Mon, 29 Jun 2020 21:49:51: 1000000 INFO @ Mon, 29 Jun 2020 21:49:57: 6000000 INFO @ Mon, 29 Jun 2020 21:49:57: 2000000 INFO @ Mon, 29 Jun 2020 21:50:03: 3000000 INFO @ Mon, 29 Jun 2020 21:50:03: 7000000 INFO @ Mon, 29 Jun 2020 21:50:08: 4000000 INFO @ Mon, 29 Jun 2020 21:50:10: 8000000 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 @ Mon, 29 Jun 2020 21:50:14: 5000000 INFO @ Mon, 29 Jun 2020 21:50:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX032119/SRX032119.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX032119/SRX032119.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX032119/SRX032119.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX032119/SRX032119.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 @ Mon, 29 Jun 2020 21:50:15: #1 read tag files... INFO @ Mon, 29 Jun 2020 21:50:15: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 21:50:17: 9000000 INFO @ Mon, 29 Jun 2020 21:50:20: 6000000 INFO @ Mon, 29 Jun 2020 21:50:22: 1000000 INFO @ Mon, 29 Jun 2020 21:50:24: 10000000 INFO @ Mon, 29 Jun 2020 21:50:27: 7000000 INFO @ Mon, 29 Jun 2020 21:50:29: 2000000 INFO @ Mon, 29 Jun 2020 21:50:32: 11000000 INFO @ Mon, 29 Jun 2020 21:50:33: 8000000 INFO @ Mon, 29 Jun 2020 21:50:36: 3000000 INFO @ Mon, 29 Jun 2020 21:50:39: 12000000 INFO @ Mon, 29 Jun 2020 21:50:39: 9000000 INFO @ Mon, 29 Jun 2020 21:50:43: 4000000 INFO @ Mon, 29 Jun 2020 21:50:45: 10000000 INFO @ Mon, 29 Jun 2020 21:50:46: 13000000 INFO @ Mon, 29 Jun 2020 21:50:51: 5000000 INFO @ Mon, 29 Jun 2020 21:50:51: 11000000 INFO @ Mon, 29 Jun 2020 21:50:53: 14000000 INFO @ Mon, 29 Jun 2020 21:50:57: 12000000 INFO @ Mon, 29 Jun 2020 21:50:58: 6000000 INFO @ Mon, 29 Jun 2020 21:51:00: 15000000 INFO @ Mon, 29 Jun 2020 21:51:03: 13000000 INFO @ Mon, 29 Jun 2020 21:51:05: 7000000 INFO @ Mon, 29 Jun 2020 21:51:07: 16000000 INFO @ Mon, 29 Jun 2020 21:51:09: 14000000 INFO @ Mon, 29 Jun 2020 21:51:12: 8000000 INFO @ Mon, 29 Jun 2020 21:51:14: 17000000 INFO @ Mon, 29 Jun 2020 21:51:16: 15000000 INFO @ Mon, 29 Jun 2020 21:51:19: 9000000 INFO @ Mon, 29 Jun 2020 21:51:21: 18000000 INFO @ Mon, 29 Jun 2020 21:51:22: 16000000 INFO @ Mon, 29 Jun 2020 21:51:26: 10000000 INFO @ Mon, 29 Jun 2020 21:51:28: 19000000 INFO @ Mon, 29 Jun 2020 21:51:28: #1 tag size is determined as 36 bps INFO @ Mon, 29 Jun 2020 21:51:28: #1 tag size = 36 INFO @ Mon, 29 Jun 2020 21:51:28: #1 total tags in treatment: 19016724 INFO @ Mon, 29 Jun 2020 21:51:28: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 21:51:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 21:51:28: #1 tags after filtering in treatment: 19016724 INFO @ Mon, 29 Jun 2020 21:51:28: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 21:51:28: #1 finished! INFO @ Mon, 29 Jun 2020 21:51:28: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 21:51:28: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 21:51:29: 17000000 INFO @ Mon, 29 Jun 2020 21:51:30: #2 number of paired peaks: 196 WARNING @ Mon, 29 Jun 2020 21:51:30: Fewer paired peaks (196) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 196 pairs to build model! INFO @ Mon, 29 Jun 2020 21:51:30: start model_add_line... INFO @ Mon, 29 Jun 2020 21:51:30: start X-correlation... INFO @ Mon, 29 Jun 2020 21:51:30: end of X-cor INFO @ Mon, 29 Jun 2020 21:51:30: #2 finished! INFO @ Mon, 29 Jun 2020 21:51:30: #2 predicted fragment length is 36 bps INFO @ Mon, 29 Jun 2020 21:51:30: #2 alternative fragment length(s) may be 36 bps INFO @ Mon, 29 Jun 2020 21:51:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX032119/SRX032119.05_model.r WARNING @ Mon, 29 Jun 2020 21:51:30: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 21:51:30: #2 You may need to consider one of the other alternative d(s): 36 WARNING @ Mon, 29 Jun 2020 21:51:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 21:51:30: #3 Call peaks... INFO @ Mon, 29 Jun 2020 21:51:30: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 21:51:33: 11000000 INFO @ Mon, 29 Jun 2020 21:51:35: 18000000 INFO @ Mon, 29 Jun 2020 21:51:39: 12000000 INFO @ Mon, 29 Jun 2020 21:51:42: 19000000 INFO @ Mon, 29 Jun 2020 21:51:42: #1 tag size is determined as 36 bps INFO @ Mon, 29 Jun 2020 21:51:42: #1 tag size = 36 INFO @ Mon, 29 Jun 2020 21:51:42: #1 total tags in treatment: 19016724 INFO @ Mon, 29 Jun 2020 21:51:42: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 21:51:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 21:51:42: #1 tags after filtering in treatment: 19016724 INFO @ Mon, 29 Jun 2020 21:51:42: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 21:51:42: #1 finished! INFO @ Mon, 29 Jun 2020 21:51:42: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 21:51:42: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 21:51:44: #2 number of paired peaks: 196 WARNING @ Mon, 29 Jun 2020 21:51:44: Fewer paired peaks (196) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 196 pairs to build model! INFO @ Mon, 29 Jun 2020 21:51:44: start model_add_line... INFO @ Mon, 29 Jun 2020 21:51:44: start X-correlation... INFO @ Mon, 29 Jun 2020 21:51:44: end of X-cor INFO @ Mon, 29 Jun 2020 21:51:44: #2 finished! INFO @ Mon, 29 Jun 2020 21:51:44: #2 predicted fragment length is 36 bps INFO @ Mon, 29 Jun 2020 21:51:44: #2 alternative fragment length(s) may be 36 bps INFO @ Mon, 29 Jun 2020 21:51:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX032119/SRX032119.10_model.r WARNING @ Mon, 29 Jun 2020 21:51:44: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 21:51:44: #2 You may need to consider one of the other alternative d(s): 36 WARNING @ Mon, 29 Jun 2020 21:51:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 21:51:44: #3 Call peaks... INFO @ Mon, 29 Jun 2020 21:51:44: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 21:51:46: 13000000 INFO @ Mon, 29 Jun 2020 21:51:53: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 21:51:59: 15000000 INFO @ Mon, 29 Jun 2020 21:52:02: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 21:52:06: 16000000 INFO @ Mon, 29 Jun 2020 21:52:13: 17000000 INFO @ Mon, 29 Jun 2020 21:52:16: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 21:52:20: 18000000 INFO @ Mon, 29 Jun 2020 21:52:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX032119/SRX032119.05_peaks.xls INFO @ Mon, 29 Jun 2020 21:52:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX032119/SRX032119.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 21:52:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX032119/SRX032119.05_summits.bed INFO @ Mon, 29 Jun 2020 21:52:20: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1871 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 21:52:26: 19000000 INFO @ Mon, 29 Jun 2020 21:52:27: #1 tag size is determined as 36 bps INFO @ Mon, 29 Jun 2020 21:52:27: #1 tag size = 36 INFO @ Mon, 29 Jun 2020 21:52:27: #1 total tags in treatment: 19016724 INFO @ Mon, 29 Jun 2020 21:52:27: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 21:52:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 21:52:27: #1 tags after filtering in treatment: 19016724 INFO @ Mon, 29 Jun 2020 21:52:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 21:52:27: #1 finished! INFO @ Mon, 29 Jun 2020 21:52:27: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 21:52:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 21:52:28: #2 number of paired peaks: 196 WARNING @ Mon, 29 Jun 2020 21:52:28: Fewer paired peaks (196) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 196 pairs to build model! INFO @ Mon, 29 Jun 2020 21:52:28: start model_add_line... INFO @ Mon, 29 Jun 2020 21:52:28: start X-correlation... INFO @ Mon, 29 Jun 2020 21:52:28: end of X-cor INFO @ Mon, 29 Jun 2020 21:52:28: #2 finished! INFO @ Mon, 29 Jun 2020 21:52:28: #2 predicted fragment length is 36 bps INFO @ Mon, 29 Jun 2020 21:52:28: #2 alternative fragment length(s) may be 36 bps INFO @ Mon, 29 Jun 2020 21:52:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX032119/SRX032119.20_model.r WARNING @ Mon, 29 Jun 2020 21:52:28: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 21:52:28: #2 You may need to consider one of the other alternative d(s): 36 WARNING @ Mon, 29 Jun 2020 21:52:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 21:52:28: #3 Call peaks... INFO @ Mon, 29 Jun 2020 21:52:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 21:52:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX032119/SRX032119.10_peaks.xls INFO @ Mon, 29 Jun 2020 21:52:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX032119/SRX032119.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 21:52:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX032119/SRX032119.10_summits.bed INFO @ Mon, 29 Jun 2020 21:52:34: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1385 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 21:53:01: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 21:53:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX032119/SRX032119.20_peaks.xls INFO @ Mon, 29 Jun 2020 21:53:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX032119/SRX032119.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 21:53:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX032119/SRX032119.20_summits.bed INFO @ Mon, 29 Jun 2020 21:53:19: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (917 records, 4 fields): 3 millis CompletedMACS2peakCalling