Job ID = 6453988 SRX = SRX1760696 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:06:54 prefetch.2.10.7: 1) Downloading 'SRR3503053'... 2020-06-21T09:06:54 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:07:59 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:08:00 prefetch.2.10.7: 'SRR3503053' is valid 2020-06-21T09:08:00 prefetch.2.10.7: 1) 'SRR3503053' was downloaded successfully 2020-06-21T09:08:00 prefetch.2.10.7: 'SRR3503053' has 0 unresolved dependencies Read 3966814 spots for SRR3503053/SRR3503053.sra Written 3966814 spots for SRR3503053/SRR3503053.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: 00:03:31 3966814 reads; of these: 3966814 (100.00%) were unpaired; of these: 1243078 (31.34%) aligned 0 times 2038084 (51.38%) aligned exactly 1 time 685652 (17.28%) aligned >1 times 68.66% overall alignment rate Time searching: 00:03:31 Overall time: 00:03:31 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_rmdupse_core] 117874 / 2723736 = 0.0433 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 18:13:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1760696/SRX1760696.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1760696/SRX1760696.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1760696/SRX1760696.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1760696/SRX1760696.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 18:13:34: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:13:34: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:13:43: 1000000 INFO @ Sun, 21 Jun 2020 18:13:52: 2000000 INFO @ Sun, 21 Jun 2020 18:13:58: #1 tag size is determined as 151 bps INFO @ Sun, 21 Jun 2020 18:13:58: #1 tag size = 151 INFO @ Sun, 21 Jun 2020 18:13:58: #1 total tags in treatment: 2605862 INFO @ Sun, 21 Jun 2020 18:13:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:13:58: #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 18:13:58: #1 tags after filtering in treatment: 2605575 INFO @ Sun, 21 Jun 2020 18:13:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:13:58: #1 finished! INFO @ Sun, 21 Jun 2020 18:13:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:13:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:13:59: #2 number of paired peaks: 828 WARNING @ Sun, 21 Jun 2020 18:13:59: Fewer paired peaks (828) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 828 pairs to build model! INFO @ Sun, 21 Jun 2020 18:13:59: start model_add_line... INFO @ Sun, 21 Jun 2020 18:13:59: start X-correlation... INFO @ Sun, 21 Jun 2020 18:13:59: end of X-cor INFO @ Sun, 21 Jun 2020 18:13:59: #2 finished! INFO @ Sun, 21 Jun 2020 18:13:59: #2 predicted fragment length is 145 bps INFO @ Sun, 21 Jun 2020 18:13:59: #2 alternative fragment length(s) may be 145 bps INFO @ Sun, 21 Jun 2020 18:13:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1760696/SRX1760696.05_model.r WARNING @ Sun, 21 Jun 2020 18:13:59: #2 Since the d (145) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:13:59: #2 You may need to consider one of the other alternative d(s): 145 WARNING @ Sun, 21 Jun 2020 18:13:59: #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 18:13:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:13:59: #3 Pre-compute pvalue-qvalue table... 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 18:14:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1760696/SRX1760696.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1760696/SRX1760696.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1760696/SRX1760696.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1760696/SRX1760696.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 18:14:04: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:14:04: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:14:05: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:14:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1760696/SRX1760696.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:14:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1760696/SRX1760696.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:14:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1760696/SRX1760696.05_summits.bed INFO @ Sun, 21 Jun 2020 18:14:08: Done! pass1 - making usageList (479 chroms): 1 millis pass2 - checking and writing primary data (1002 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:14:11: 1000000 INFO @ Sun, 21 Jun 2020 18:14:19: 2000000 INFO @ Sun, 21 Jun 2020 18:14:24: #1 tag size is determined as 151 bps INFO @ Sun, 21 Jun 2020 18:14:24: #1 tag size = 151 INFO @ Sun, 21 Jun 2020 18:14:24: #1 total tags in treatment: 2605862 INFO @ Sun, 21 Jun 2020 18:14:24: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:14:24: #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 18:14:24: #1 tags after filtering in treatment: 2605575 INFO @ Sun, 21 Jun 2020 18:14:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:14:24: #1 finished! INFO @ Sun, 21 Jun 2020 18:14:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:14:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:14:24: #2 number of paired peaks: 828 WARNING @ Sun, 21 Jun 2020 18:14:24: Fewer paired peaks (828) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 828 pairs to build model! INFO @ Sun, 21 Jun 2020 18:14:24: start model_add_line... INFO @ Sun, 21 Jun 2020 18:14:24: start X-correlation... INFO @ Sun, 21 Jun 2020 18:14:24: end of X-cor INFO @ Sun, 21 Jun 2020 18:14:24: #2 finished! INFO @ Sun, 21 Jun 2020 18:14:24: #2 predicted fragment length is 145 bps INFO @ Sun, 21 Jun 2020 18:14:24: #2 alternative fragment length(s) may be 145 bps INFO @ Sun, 21 Jun 2020 18:14:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1760696/SRX1760696.10_model.r WARNING @ Sun, 21 Jun 2020 18:14:24: #2 Since the d (145) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:14:24: #2 You may need to consider one of the other alternative d(s): 145 WARNING @ Sun, 21 Jun 2020 18:14:24: #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 18:14:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:14:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:14:30: #3 Call peaks for each chromosome... 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 18:14:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1760696/SRX1760696.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:14:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1760696/SRX1760696.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:14:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1760696/SRX1760696.10_summits.bed INFO @ Sun, 21 Jun 2020 18:14:33: Done! pass1 - making usageList (383 chroms): 1 millis pass2 - checking and writing primary data (678 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:14:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1760696/SRX1760696.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1760696/SRX1760696.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1760696/SRX1760696.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1760696/SRX1760696.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 18:14:34: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:14:34: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:14:43: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:14:52: 2000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:14:58: #1 tag size is determined as 151 bps INFO @ Sun, 21 Jun 2020 18:14:58: #1 tag size = 151 INFO @ Sun, 21 Jun 2020 18:14:58: #1 total tags in treatment: 2605862 INFO @ Sun, 21 Jun 2020 18:14:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:14:58: #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 18:14:58: #1 tags after filtering in treatment: 2605575 INFO @ Sun, 21 Jun 2020 18:14:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:14:58: #1 finished! INFO @ Sun, 21 Jun 2020 18:14:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:14:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:14:58: #2 number of paired peaks: 828 WARNING @ Sun, 21 Jun 2020 18:14:58: Fewer paired peaks (828) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 828 pairs to build model! INFO @ Sun, 21 Jun 2020 18:14:58: start model_add_line... INFO @ Sun, 21 Jun 2020 18:14:58: start X-correlation... INFO @ Sun, 21 Jun 2020 18:14:59: end of X-cor INFO @ Sun, 21 Jun 2020 18:14:59: #2 finished! INFO @ Sun, 21 Jun 2020 18:14:59: #2 predicted fragment length is 145 bps INFO @ Sun, 21 Jun 2020 18:14:59: #2 alternative fragment length(s) may be 145 bps INFO @ Sun, 21 Jun 2020 18:14:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1760696/SRX1760696.20_model.r WARNING @ Sun, 21 Jun 2020 18:14:59: #2 Since the d (145) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:14:59: #2 You may need to consider one of the other alternative d(s): 145 WARNING @ Sun, 21 Jun 2020 18:14:59: #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 18:14:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:14:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:15:05: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:15:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1760696/SRX1760696.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:15:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1760696/SRX1760696.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:15:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1760696/SRX1760696.20_summits.bed INFO @ Sun, 21 Jun 2020 18:15:07: Done! pass1 - making usageList (257 chroms): 1 millis pass2 - checking and writing primary data (349 records, 4 fields): 8 millis CompletedMACS2peakCalling