Job ID = 6527585 SRX = SRX1167419 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T12:50:13 prefetch.2.10.7: 1) Downloading 'SRR2192443'... 2020-06-29T12:50:13 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:53:40 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:53:40 prefetch.2.10.7: 1) 'SRR2192443' was downloaded successfully Read 37699681 spots for SRR2192443/SRR2192443.sra Written 37699681 spots for SRR2192443/SRR2192443.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: 00:21:33 37699681 reads; of these: 37699681 (100.00%) were unpaired; of these: 767784 (2.04%) aligned 0 times 12396728 (32.88%) aligned exactly 1 time 24535169 (65.08%) aligned >1 times 97.96% overall alignment rate Time searching: 00:21:33 Overall time: 00:21:33 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 16 files... [bam_rmdupse_core] 8146544 / 36931897 = 0.2206 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 22:41:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1167419/SRX1167419.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1167419/SRX1167419.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1167419/SRX1167419.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1167419/SRX1167419.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 22:41:06: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:41:06: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:41:11: 1000000 INFO @ Mon, 29 Jun 2020 22:41:16: 2000000 INFO @ Mon, 29 Jun 2020 22:41:21: 3000000 INFO @ Mon, 29 Jun 2020 22:41:26: 4000000 INFO @ Mon, 29 Jun 2020 22:41:32: 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 @ Mon, 29 Jun 2020 22:41:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1167419/SRX1167419.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1167419/SRX1167419.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1167419/SRX1167419.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1167419/SRX1167419.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 22:41:36: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:41:36: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:41:37: 6000000 INFO @ Mon, 29 Jun 2020 22:41:42: 1000000 INFO @ Mon, 29 Jun 2020 22:41:42: 7000000 INFO @ Mon, 29 Jun 2020 22:41:48: 2000000 INFO @ Mon, 29 Jun 2020 22:41:48: 8000000 INFO @ Mon, 29 Jun 2020 22:41:53: 3000000 INFO @ Mon, 29 Jun 2020 22:41:54: 9000000 INFO @ Mon, 29 Jun 2020 22:41:59: 4000000 INFO @ Mon, 29 Jun 2020 22:41:59: 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 @ Mon, 29 Jun 2020 22:42:04: 5000000 INFO @ Mon, 29 Jun 2020 22:42:05: 11000000 INFO @ Mon, 29 Jun 2020 22:42:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1167419/SRX1167419.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1167419/SRX1167419.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1167419/SRX1167419.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1167419/SRX1167419.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 22:42:06: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:42:06: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:42:10: 6000000 INFO @ Mon, 29 Jun 2020 22:42:10: 12000000 INFO @ Mon, 29 Jun 2020 22:42:11: 1000000 INFO @ Mon, 29 Jun 2020 22:42:15: 7000000 INFO @ Mon, 29 Jun 2020 22:42:16: 13000000 INFO @ Mon, 29 Jun 2020 22:42:17: 2000000 INFO @ Mon, 29 Jun 2020 22:42:21: 8000000 INFO @ Mon, 29 Jun 2020 22:42:22: 14000000 INFO @ Mon, 29 Jun 2020 22:42:22: 3000000 INFO @ Mon, 29 Jun 2020 22:42:27: 9000000 INFO @ Mon, 29 Jun 2020 22:42:27: 15000000 INFO @ Mon, 29 Jun 2020 22:42:27: 4000000 INFO @ Mon, 29 Jun 2020 22:42:32: 5000000 INFO @ Mon, 29 Jun 2020 22:42:32: 16000000 INFO @ Mon, 29 Jun 2020 22:42:32: 10000000 INFO @ Mon, 29 Jun 2020 22:42:38: 6000000 INFO @ Mon, 29 Jun 2020 22:42:38: 17000000 INFO @ Mon, 29 Jun 2020 22:42:38: 11000000 INFO @ Mon, 29 Jun 2020 22:42:43: 7000000 INFO @ Mon, 29 Jun 2020 22:42:43: 18000000 INFO @ Mon, 29 Jun 2020 22:42:44: 12000000 INFO @ Mon, 29 Jun 2020 22:42:48: 8000000 INFO @ Mon, 29 Jun 2020 22:42:49: 19000000 INFO @ Mon, 29 Jun 2020 22:42:50: 13000000 INFO @ Mon, 29 Jun 2020 22:42:53: 9000000 INFO @ Mon, 29 Jun 2020 22:42:54: 20000000 INFO @ Mon, 29 Jun 2020 22:42:55: 14000000 INFO @ Mon, 29 Jun 2020 22:42:58: 10000000 INFO @ Mon, 29 Jun 2020 22:43:00: 21000000 INFO @ Mon, 29 Jun 2020 22:43:01: 15000000 INFO @ Mon, 29 Jun 2020 22:43:04: 11000000 INFO @ Mon, 29 Jun 2020 22:43:06: 22000000 INFO @ Mon, 29 Jun 2020 22:43:07: 16000000 INFO @ Mon, 29 Jun 2020 22:43:09: 12000000 INFO @ Mon, 29 Jun 2020 22:43:12: 23000000 INFO @ Mon, 29 Jun 2020 22:43:12: 17000000 INFO @ Mon, 29 Jun 2020 22:43:14: 13000000 INFO @ Mon, 29 Jun 2020 22:43:18: 24000000 INFO @ Mon, 29 Jun 2020 22:43:18: 18000000 INFO @ Mon, 29 Jun 2020 22:43:20: 14000000 INFO @ Mon, 29 Jun 2020 22:43:24: 25000000 INFO @ Mon, 29 Jun 2020 22:43:24: 19000000 INFO @ Mon, 29 Jun 2020 22:43:25: 15000000 INFO @ Mon, 29 Jun 2020 22:43:30: 26000000 INFO @ Mon, 29 Jun 2020 22:43:30: 20000000 INFO @ Mon, 29 Jun 2020 22:43:30: 16000000 INFO @ Mon, 29 Jun 2020 22:43:35: 27000000 INFO @ Mon, 29 Jun 2020 22:43:36: 17000000 INFO @ Mon, 29 Jun 2020 22:43:36: 21000000 INFO @ Mon, 29 Jun 2020 22:43:41: 18000000 INFO @ Mon, 29 Jun 2020 22:43:41: 28000000 INFO @ Mon, 29 Jun 2020 22:43:42: 22000000 INFO @ Mon, 29 Jun 2020 22:43:46: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 22:43:46: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 22:43:46: #1 total tags in treatment: 28785353 INFO @ Mon, 29 Jun 2020 22:43:46: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:43:46: #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 22:43:46: 19000000 INFO @ Mon, 29 Jun 2020 22:43:47: #1 tags after filtering in treatment: 28785353 INFO @ Mon, 29 Jun 2020 22:43:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:43:47: #1 finished! INFO @ Mon, 29 Jun 2020 22:43:47: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:43:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:43:47: 23000000 INFO @ Mon, 29 Jun 2020 22:43:49: #2 number of paired peaks: 170 WARNING @ Mon, 29 Jun 2020 22:43:49: Fewer paired peaks (170) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 170 pairs to build model! INFO @ Mon, 29 Jun 2020 22:43:49: start model_add_line... INFO @ Mon, 29 Jun 2020 22:43:49: start X-correlation... INFO @ Mon, 29 Jun 2020 22:43:49: end of X-cor INFO @ Mon, 29 Jun 2020 22:43:49: #2 finished! INFO @ Mon, 29 Jun 2020 22:43:49: #2 predicted fragment length is 39 bps INFO @ Mon, 29 Jun 2020 22:43:49: #2 alternative fragment length(s) may be 3,39 bps INFO @ Mon, 29 Jun 2020 22:43:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1167419/SRX1167419.05_model.r WARNING @ Mon, 29 Jun 2020 22:43:49: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:43:49: #2 You may need to consider one of the other alternative d(s): 3,39 WARNING @ Mon, 29 Jun 2020 22:43:49: #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 22:43:49: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:43:49: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:43:51: 20000000 INFO @ Mon, 29 Jun 2020 22:43:53: 24000000 INFO @ Mon, 29 Jun 2020 22:43:56: 21000000 INFO @ Mon, 29 Jun 2020 22:43:58: 25000000 INFO @ Mon, 29 Jun 2020 22:44:02: 22000000 INFO @ Mon, 29 Jun 2020 22:44:03: 26000000 INFO @ Mon, 29 Jun 2020 22:44:07: 23000000 INFO @ Mon, 29 Jun 2020 22:44:08: 27000000 INFO @ Mon, 29 Jun 2020 22:44:12: 24000000 INFO @ Mon, 29 Jun 2020 22:44:14: 28000000 INFO @ Mon, 29 Jun 2020 22:44:17: 25000000 INFO @ Mon, 29 Jun 2020 22:44:18: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 22:44:18: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 22:44:18: #1 total tags in treatment: 28785353 INFO @ Mon, 29 Jun 2020 22:44:18: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:44:18: #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 22:44:19: #1 tags after filtering in treatment: 28785353 INFO @ Mon, 29 Jun 2020 22:44:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:44:19: #1 finished! INFO @ Mon, 29 Jun 2020 22:44:19: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:44:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:44:20: #2 number of paired peaks: 170 WARNING @ Mon, 29 Jun 2020 22:44:20: Fewer paired peaks (170) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 170 pairs to build model! INFO @ Mon, 29 Jun 2020 22:44:20: start model_add_line... INFO @ Mon, 29 Jun 2020 22:44:21: start X-correlation... INFO @ Mon, 29 Jun 2020 22:44:21: end of X-cor INFO @ Mon, 29 Jun 2020 22:44:21: #2 finished! INFO @ Mon, 29 Jun 2020 22:44:21: #2 predicted fragment length is 39 bps INFO @ Mon, 29 Jun 2020 22:44:21: #2 alternative fragment length(s) may be 3,39 bps INFO @ Mon, 29 Jun 2020 22:44:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1167419/SRX1167419.10_model.r WARNING @ Mon, 29 Jun 2020 22:44:21: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:44:21: #2 You may need to consider one of the other alternative d(s): 3,39 WARNING @ Mon, 29 Jun 2020 22:44:21: #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 22:44:21: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:44:21: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:44:22: 26000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 22:44:27: 27000000 INFO @ Mon, 29 Jun 2020 22:44:32: 28000000 INFO @ Mon, 29 Jun 2020 22:44:34: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:44:36: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 22:44:36: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 22:44:36: #1 total tags in treatment: 28785353 INFO @ Mon, 29 Jun 2020 22:44:36: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:44:36: #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 22:44:37: #1 tags after filtering in treatment: 28785353 INFO @ Mon, 29 Jun 2020 22:44:37: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:44:37: #1 finished! INFO @ Mon, 29 Jun 2020 22:44:37: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:44:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:44:39: #2 number of paired peaks: 170 WARNING @ Mon, 29 Jun 2020 22:44:39: Fewer paired peaks (170) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 170 pairs to build model! INFO @ Mon, 29 Jun 2020 22:44:39: start model_add_line... INFO @ Mon, 29 Jun 2020 22:44:39: start X-correlation... INFO @ Mon, 29 Jun 2020 22:44:39: end of X-cor INFO @ Mon, 29 Jun 2020 22:44:39: #2 finished! INFO @ Mon, 29 Jun 2020 22:44:39: #2 predicted fragment length is 39 bps INFO @ Mon, 29 Jun 2020 22:44:39: #2 alternative fragment length(s) may be 3,39 bps INFO @ Mon, 29 Jun 2020 22:44:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1167419/SRX1167419.20_model.r WARNING @ Mon, 29 Jun 2020 22:44:39: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:44:39: #2 You may need to consider one of the other alternative d(s): 3,39 WARNING @ Mon, 29 Jun 2020 22:44:39: #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 22:44:39: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:44:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:44:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1167419/SRX1167419.05_peaks.xls INFO @ Mon, 29 Jun 2020 22:44:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1167419/SRX1167419.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:44:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1167419/SRX1167419.05_summits.bed INFO @ Mon, 29 Jun 2020 22:44:58: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5784 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:45:06: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:45:23: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:45:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1167419/SRX1167419.10_peaks.xls INFO @ Mon, 29 Jun 2020 22:45:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1167419/SRX1167419.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:45:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1167419/SRX1167419.10_summits.bed INFO @ Mon, 29 Jun 2020 22:45:30: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (2087 records, 4 fields): 4 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 22:45:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1167419/SRX1167419.20_peaks.xls INFO @ Mon, 29 Jun 2020 22:45:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1167419/SRX1167419.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:45:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1167419/SRX1167419.20_summits.bed INFO @ Mon, 29 Jun 2020 22:45:45: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (985 records, 4 fields): 3 millis CompletedMACS2peakCalling