Job ID = 6527610 SRX = SRX1361353 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T13:03:36 prefetch.2.10.7: 1) Downloading 'SRR2749791'... 2020-06-29T13:03:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:07:34 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:07:34 prefetch.2.10.7: 1) 'SRR2749791' was downloaded successfully Read 29500321 spots for SRR2749791/SRR2749791.sra Written 29500321 spots for SRR2749791/SRR2749791.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: 00:13:17 29500321 reads; of these: 29500321 (100.00%) were unpaired; of these: 1783363 (6.05%) aligned 0 times 14969334 (50.74%) aligned exactly 1 time 12747624 (43.21%) aligned >1 times 93.95% overall alignment rate Time searching: 00:13:17 Overall time: 00:13:17 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 12 files... [bam_rmdupse_core] 5939255 / 27716958 = 0.2143 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 22:37:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1361353/SRX1361353.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1361353/SRX1361353.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1361353/SRX1361353.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1361353/SRX1361353.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 22:37:32: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:37:32: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:37:39: 1000000 INFO @ Mon, 29 Jun 2020 22:37:46: 2000000 INFO @ Mon, 29 Jun 2020 22:37:52: 3000000 INFO @ Mon, 29 Jun 2020 22:37:59: 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 @ Mon, 29 Jun 2020 22:38:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1361353/SRX1361353.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1361353/SRX1361353.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1361353/SRX1361353.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1361353/SRX1361353.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 22:38:02: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:38:02: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:38:06: 5000000 INFO @ Mon, 29 Jun 2020 22:38:08: 1000000 INFO @ Mon, 29 Jun 2020 22:38:13: 6000000 INFO @ Mon, 29 Jun 2020 22:38:15: 2000000 INFO @ Mon, 29 Jun 2020 22:38:21: 7000000 INFO @ Mon, 29 Jun 2020 22:38:21: 3000000 INFO @ Mon, 29 Jun 2020 22:38:28: 4000000 INFO @ Mon, 29 Jun 2020 22:38:28: 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 22:38:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1361353/SRX1361353.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1361353/SRX1361353.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1361353/SRX1361353.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1361353/SRX1361353.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 22:38:32: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:38:32: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:38:34: 5000000 INFO @ Mon, 29 Jun 2020 22:38:36: 9000000 INFO @ Mon, 29 Jun 2020 22:38:39: 1000000 INFO @ Mon, 29 Jun 2020 22:38:41: 6000000 INFO @ Mon, 29 Jun 2020 22:38:43: 10000000 INFO @ Mon, 29 Jun 2020 22:38:46: 2000000 INFO @ Mon, 29 Jun 2020 22:38:48: 7000000 INFO @ Mon, 29 Jun 2020 22:38:51: 11000000 INFO @ Mon, 29 Jun 2020 22:38:54: 3000000 INFO @ Mon, 29 Jun 2020 22:38:54: 8000000 INFO @ Mon, 29 Jun 2020 22:38:58: 12000000 INFO @ Mon, 29 Jun 2020 22:39:01: 9000000 INFO @ Mon, 29 Jun 2020 22:39:01: 4000000 INFO @ Mon, 29 Jun 2020 22:39:06: 13000000 INFO @ Mon, 29 Jun 2020 22:39:08: 10000000 INFO @ Mon, 29 Jun 2020 22:39:09: 5000000 INFO @ Mon, 29 Jun 2020 22:39:13: 14000000 INFO @ Mon, 29 Jun 2020 22:39:14: 11000000 INFO @ Mon, 29 Jun 2020 22:39:16: 6000000 INFO @ Mon, 29 Jun 2020 22:39:21: 15000000 INFO @ Mon, 29 Jun 2020 22:39:21: 12000000 INFO @ Mon, 29 Jun 2020 22:39:23: 7000000 INFO @ Mon, 29 Jun 2020 22:39:28: 13000000 INFO @ Mon, 29 Jun 2020 22:39:28: 16000000 INFO @ Mon, 29 Jun 2020 22:39:31: 8000000 INFO @ Mon, 29 Jun 2020 22:39:35: 14000000 INFO @ Mon, 29 Jun 2020 22:39:36: 17000000 INFO @ Mon, 29 Jun 2020 22:39:39: 9000000 INFO @ Mon, 29 Jun 2020 22:39:41: 15000000 INFO @ Mon, 29 Jun 2020 22:39:43: 18000000 INFO @ Mon, 29 Jun 2020 22:39:46: 10000000 INFO @ Mon, 29 Jun 2020 22:39:48: 16000000 INFO @ Mon, 29 Jun 2020 22:39:51: 19000000 INFO @ Mon, 29 Jun 2020 22:39:54: 11000000 INFO @ Mon, 29 Jun 2020 22:39:55: 17000000 INFO @ Mon, 29 Jun 2020 22:39:58: 20000000 INFO @ Mon, 29 Jun 2020 22:40:02: 18000000 INFO @ Mon, 29 Jun 2020 22:40:02: 12000000 INFO @ Mon, 29 Jun 2020 22:40:06: 21000000 INFO @ Mon, 29 Jun 2020 22:40:08: 19000000 INFO @ Mon, 29 Jun 2020 22:40:10: 13000000 INFO @ Mon, 29 Jun 2020 22:40:12: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 22:40:12: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 22:40:12: #1 total tags in treatment: 21777703 INFO @ Mon, 29 Jun 2020 22:40:12: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:40:12: #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 22:40:12: #1 tags after filtering in treatment: 21777703 INFO @ Mon, 29 Jun 2020 22:40:12: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:40:12: #1 finished! INFO @ Mon, 29 Jun 2020 22:40:12: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:40:12: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 22:40:14: #2 number of paired peaks: 274 WARNING @ Mon, 29 Jun 2020 22:40:14: Fewer paired peaks (274) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 274 pairs to build model! INFO @ Mon, 29 Jun 2020 22:40:14: start model_add_line... INFO @ Mon, 29 Jun 2020 22:40:14: start X-correlation... INFO @ Mon, 29 Jun 2020 22:40:14: end of X-cor INFO @ Mon, 29 Jun 2020 22:40:14: #2 finished! INFO @ Mon, 29 Jun 2020 22:40:14: #2 predicted fragment length is 49 bps INFO @ Mon, 29 Jun 2020 22:40:14: #2 alternative fragment length(s) may be 2,49 bps INFO @ Mon, 29 Jun 2020 22:40:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1361353/SRX1361353.05_model.r WARNING @ Mon, 29 Jun 2020 22:40:14: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:40:14: #2 You may need to consider one of the other alternative d(s): 2,49 WARNING @ Mon, 29 Jun 2020 22:40:14: #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 22:40:14: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:40:14: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:40:15: 20000000 INFO @ Mon, 29 Jun 2020 22:40:18: 14000000 INFO @ Mon, 29 Jun 2020 22:40:22: 21000000 INFO @ Mon, 29 Jun 2020 22:40:25: 15000000 INFO @ Mon, 29 Jun 2020 22:40:27: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 22:40:27: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 22:40:27: #1 total tags in treatment: 21777703 INFO @ Mon, 29 Jun 2020 22:40:27: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:40:27: #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 22:40:28: #1 tags after filtering in treatment: 21777703 INFO @ Mon, 29 Jun 2020 22:40:28: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:40:28: #1 finished! INFO @ Mon, 29 Jun 2020 22:40:28: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:40:28: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:40:29: #2 number of paired peaks: 274 WARNING @ Mon, 29 Jun 2020 22:40:29: Fewer paired peaks (274) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 274 pairs to build model! INFO @ Mon, 29 Jun 2020 22:40:29: start model_add_line... INFO @ Mon, 29 Jun 2020 22:40:29: start X-correlation... INFO @ Mon, 29 Jun 2020 22:40:29: end of X-cor INFO @ Mon, 29 Jun 2020 22:40:29: #2 finished! INFO @ Mon, 29 Jun 2020 22:40:29: #2 predicted fragment length is 49 bps INFO @ Mon, 29 Jun 2020 22:40:29: #2 alternative fragment length(s) may be 2,49 bps INFO @ Mon, 29 Jun 2020 22:40:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1361353/SRX1361353.10_model.r WARNING @ Mon, 29 Jun 2020 22:40:29: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:40:29: #2 You may need to consider one of the other alternative d(s): 2,49 WARNING @ Mon, 29 Jun 2020 22:40:29: #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 22:40:29: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:40:29: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:40:32: 16000000 INFO @ Mon, 29 Jun 2020 22:40:39: 17000000 INFO @ Mon, 29 Jun 2020 22:40:46: 18000000 INFO @ Mon, 29 Jun 2020 22:40:53: 19000000 INFO @ Mon, 29 Jun 2020 22:40:58: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:41:00: 20000000 BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 22:41:07: 21000000 INFO @ Mon, 29 Jun 2020 22:41:12: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 22:41:12: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 22:41:12: #1 total tags in treatment: 21777703 INFO @ Mon, 29 Jun 2020 22:41:12: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:41:12: #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 22:41:12: #1 tags after filtering in treatment: 21777703 INFO @ Mon, 29 Jun 2020 22:41:12: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:41:12: #1 finished! INFO @ Mon, 29 Jun 2020 22:41:12: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:41:12: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:41:13: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:41:14: #2 number of paired peaks: 274 WARNING @ Mon, 29 Jun 2020 22:41:14: Fewer paired peaks (274) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 274 pairs to build model! INFO @ Mon, 29 Jun 2020 22:41:14: start model_add_line... INFO @ Mon, 29 Jun 2020 22:41:14: start X-correlation... INFO @ Mon, 29 Jun 2020 22:41:14: end of X-cor INFO @ Mon, 29 Jun 2020 22:41:14: #2 finished! INFO @ Mon, 29 Jun 2020 22:41:14: #2 predicted fragment length is 49 bps INFO @ Mon, 29 Jun 2020 22:41:14: #2 alternative fragment length(s) may be 2,49 bps INFO @ Mon, 29 Jun 2020 22:41:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1361353/SRX1361353.20_model.r WARNING @ Mon, 29 Jun 2020 22:41:14: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:41:14: #2 You may need to consider one of the other alternative d(s): 2,49 WARNING @ Mon, 29 Jun 2020 22:41:14: #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 22:41:14: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:41:14: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:41:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1361353/SRX1361353.05_peaks.xls INFO @ Mon, 29 Jun 2020 22:41:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1361353/SRX1361353.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:41:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1361353/SRX1361353.05_summits.bed INFO @ Mon, 29 Jun 2020 22:41:21: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (8308 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:41:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1361353/SRX1361353.10_peaks.xls INFO @ Mon, 29 Jun 2020 22:41:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1361353/SRX1361353.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:41:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1361353/SRX1361353.10_summits.bed INFO @ Mon, 29 Jun 2020 22:41:35: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2131 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:41:57: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:42:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1361353/SRX1361353.20_peaks.xls INFO @ Mon, 29 Jun 2020 22:42:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1361353/SRX1361353.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:42:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1361353/SRX1361353.20_summits.bed INFO @ Mon, 29 Jun 2020 22:42:18: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (1113 records, 4 fields): 3 millis CompletedMACS2peakCalling