Job ID = 6498293 SRX = SRX467104 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T23:32:16 prefetch.2.10.7: 1) Downloading 'SRR1164528'... 2020-06-25T23:32:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T23:35:43 prefetch.2.10.7: HTTPS download succeed 2020-06-25T23:35:43 prefetch.2.10.7: 1) 'SRR1164528' was downloaded successfully Read 16856264 spots for SRR1164528/SRR1164528.sra Written 16856264 spots for SRR1164528/SRR1164528.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:30 16856264 reads; of these: 16856264 (100.00%) were unpaired; of these: 886514 (5.26%) aligned 0 times 11886690 (70.52%) aligned exactly 1 time 4083060 (24.22%) aligned >1 times 94.74% overall alignment rate Time searching: 00:06:31 Overall time: 00:06:31 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] 1505141 / 15969750 = 0.0942 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 @ Fri, 26 Jun 2020 08:47:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467104/SRX467104.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467104/SRX467104.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467104/SRX467104.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467104/SRX467104.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 @ Fri, 26 Jun 2020 08:47:51: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:47:51: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:47:57: 1000000 INFO @ Fri, 26 Jun 2020 08:48:03: 2000000 INFO @ Fri, 26 Jun 2020 08:48:09: 3000000 INFO @ Fri, 26 Jun 2020 08:48:16: 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 @ Fri, 26 Jun 2020 08:48:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467104/SRX467104.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467104/SRX467104.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467104/SRX467104.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467104/SRX467104.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 @ Fri, 26 Jun 2020 08:48:20: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:48:20: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:48:22: 5000000 INFO @ Fri, 26 Jun 2020 08:48:27: 1000000 INFO @ Fri, 26 Jun 2020 08:48:29: 6000000 INFO @ Fri, 26 Jun 2020 08:48:34: 2000000 INFO @ Fri, 26 Jun 2020 08:48:36: 7000000 INFO @ Fri, 26 Jun 2020 08:48:40: 3000000 INFO @ Fri, 26 Jun 2020 08:48:42: 8000000 INFO @ Fri, 26 Jun 2020 08:48:47: 4000000 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 @ Fri, 26 Jun 2020 08:48:49: 9000000 INFO @ Fri, 26 Jun 2020 08:48:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467104/SRX467104.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467104/SRX467104.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467104/SRX467104.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467104/SRX467104.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 @ Fri, 26 Jun 2020 08:48:50: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:48:50: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:48:53: 5000000 INFO @ Fri, 26 Jun 2020 08:48:55: 10000000 INFO @ Fri, 26 Jun 2020 08:48:57: 1000000 INFO @ Fri, 26 Jun 2020 08:48:59: 6000000 INFO @ Fri, 26 Jun 2020 08:49:02: 11000000 INFO @ Fri, 26 Jun 2020 08:49:03: 2000000 INFO @ Fri, 26 Jun 2020 08:49:06: 7000000 INFO @ Fri, 26 Jun 2020 08:49:08: 12000000 INFO @ Fri, 26 Jun 2020 08:49:10: 3000000 INFO @ Fri, 26 Jun 2020 08:49:12: 8000000 INFO @ Fri, 26 Jun 2020 08:49:15: 13000000 INFO @ Fri, 26 Jun 2020 08:49:16: 4000000 INFO @ Fri, 26 Jun 2020 08:49:18: 9000000 INFO @ Fri, 26 Jun 2020 08:49:21: 14000000 INFO @ Fri, 26 Jun 2020 08:49:23: 5000000 INFO @ Fri, 26 Jun 2020 08:49:24: 10000000 INFO @ Fri, 26 Jun 2020 08:49:24: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:49:24: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:49:24: #1 total tags in treatment: 14464609 INFO @ Fri, 26 Jun 2020 08:49:24: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:49:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:49:25: #1 tags after filtering in treatment: 14464609 INFO @ Fri, 26 Jun 2020 08:49:25: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:49:25: #1 finished! INFO @ Fri, 26 Jun 2020 08:49:25: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:49:25: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:49:26: #2 number of paired peaks: 128 WARNING @ Fri, 26 Jun 2020 08:49:26: 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 @ Fri, 26 Jun 2020 08:49:26: start model_add_line... INFO @ Fri, 26 Jun 2020 08:49:26: start X-correlation... INFO @ Fri, 26 Jun 2020 08:49:26: end of X-cor INFO @ Fri, 26 Jun 2020 08:49:26: #2 finished! INFO @ Fri, 26 Jun 2020 08:49:26: #2 predicted fragment length is 46 bps INFO @ Fri, 26 Jun 2020 08:49:26: #2 alternative fragment length(s) may be 46 bps INFO @ Fri, 26 Jun 2020 08:49:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX467104/SRX467104.05_model.r WARNING @ Fri, 26 Jun 2020 08:49:26: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 08:49:26: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Fri, 26 Jun 2020 08:49:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 08:49:26: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:49:26: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:49:29: 6000000 INFO @ Fri, 26 Jun 2020 08:49:30: 11000000 INFO @ Fri, 26 Jun 2020 08:49:35: 7000000 INFO @ Fri, 26 Jun 2020 08:49:37: 12000000 INFO @ Fri, 26 Jun 2020 08:49:42: 8000000 INFO @ Fri, 26 Jun 2020 08:49:43: 13000000 INFO @ Fri, 26 Jun 2020 08:49:48: 9000000 INFO @ Fri, 26 Jun 2020 08:49:49: 14000000 INFO @ Fri, 26 Jun 2020 08:49:53: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:49:53: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:49:53: #1 total tags in treatment: 14464609 INFO @ Fri, 26 Jun 2020 08:49:53: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:49:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:49:53: #1 tags after filtering in treatment: 14464609 INFO @ Fri, 26 Jun 2020 08:49:53: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:49:53: #1 finished! INFO @ Fri, 26 Jun 2020 08:49:53: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:49:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:49:54: #2 number of paired peaks: 128 WARNING @ Fri, 26 Jun 2020 08:49:54: 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 @ Fri, 26 Jun 2020 08:49:54: start model_add_line... INFO @ Fri, 26 Jun 2020 08:49:54: start X-correlation... INFO @ Fri, 26 Jun 2020 08:49:54: end of X-cor INFO @ Fri, 26 Jun 2020 08:49:54: #2 finished! INFO @ Fri, 26 Jun 2020 08:49:54: #2 predicted fragment length is 46 bps INFO @ Fri, 26 Jun 2020 08:49:54: #2 alternative fragment length(s) may be 46 bps INFO @ Fri, 26 Jun 2020 08:49:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX467104/SRX467104.10_model.r WARNING @ Fri, 26 Jun 2020 08:49:54: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 08:49:54: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Fri, 26 Jun 2020 08:49:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 08:49:54: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:49:54: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:49:54: 10000000 INFO @ Fri, 26 Jun 2020 08:49:56: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:50:00: 11000000 INFO @ Fri, 26 Jun 2020 08:50:06: 12000000 INFO @ Fri, 26 Jun 2020 08:50:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX467104/SRX467104.05_peaks.xls INFO @ Fri, 26 Jun 2020 08:50:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX467104/SRX467104.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:50:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX467104/SRX467104.05_summits.bed INFO @ Fri, 26 Jun 2020 08:50:11: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1911 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:50:12: 13000000 INFO @ Fri, 26 Jun 2020 08:50:17: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 08:50:20: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:50:20: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:50:20: #1 total tags in treatment: 14464609 INFO @ Fri, 26 Jun 2020 08:50:20: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:50:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:50:20: #1 tags after filtering in treatment: 14464609 INFO @ Fri, 26 Jun 2020 08:50:20: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:50:20: #1 finished! INFO @ Fri, 26 Jun 2020 08:50:20: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:50:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:50:21: #2 number of paired peaks: 128 WARNING @ Fri, 26 Jun 2020 08:50:21: 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 @ Fri, 26 Jun 2020 08:50:21: start model_add_line... INFO @ Fri, 26 Jun 2020 08:50:21: start X-correlation... INFO @ Fri, 26 Jun 2020 08:50:21: end of X-cor INFO @ Fri, 26 Jun 2020 08:50:21: #2 finished! INFO @ Fri, 26 Jun 2020 08:50:21: #2 predicted fragment length is 46 bps INFO @ Fri, 26 Jun 2020 08:50:21: #2 alternative fragment length(s) may be 46 bps INFO @ Fri, 26 Jun 2020 08:50:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX467104/SRX467104.20_model.r WARNING @ Fri, 26 Jun 2020 08:50:21: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 08:50:21: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Fri, 26 Jun 2020 08:50:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 08:50:21: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:50:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:50:24: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:50:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX467104/SRX467104.10_peaks.xls INFO @ Fri, 26 Jun 2020 08:50:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX467104/SRX467104.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:50:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX467104/SRX467104.10_summits.bed INFO @ Fri, 26 Jun 2020 08:50:39: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1636 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:50:51: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 08:51:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX467104/SRX467104.20_peaks.xls INFO @ Fri, 26 Jun 2020 08:51:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX467104/SRX467104.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:51:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX467104/SRX467104.20_summits.bed INFO @ Fri, 26 Jun 2020 08:51:05: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1193 records, 4 fields): 7 millis CompletedMACS2peakCalling