Job ID = 6456492 SRX = SRX3511943 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:52:46 prefetch.2.10.7: 1) Downloading 'SRR6418928'... 2020-06-21T10:52:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:55:56 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:55:57 prefetch.2.10.7: 'SRR6418928' is valid 2020-06-21T10:55:57 prefetch.2.10.7: 1) 'SRR6418928' was downloaded successfully 2020-06-21T10:55:57 prefetch.2.10.7: 'SRR6418928' has 0 unresolved dependencies Read 10879524 spots for SRR6418928/SRR6418928.sra Written 10879524 spots for SRR6418928/SRR6418928.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: 00:05:06 10879524 reads; of these: 10879524 (100.00%) were unpaired; of these: 1061610 (9.76%) aligned 0 times 7511857 (69.05%) aligned exactly 1 time 2306057 (21.20%) aligned >1 times 90.24% overall alignment rate Time searching: 00:05:06 Overall time: 00:05:06 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] 686545 / 9817914 = 0.0699 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 20:06:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3511943/SRX3511943.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3511943/SRX3511943.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3511943/SRX3511943.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3511943/SRX3511943.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 20:06:59: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:06:59: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:07:08: 1000000 INFO @ Sun, 21 Jun 2020 20:07:17: 2000000 INFO @ Sun, 21 Jun 2020 20:07:26: 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 @ Sun, 21 Jun 2020 20:07:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3511943/SRX3511943.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3511943/SRX3511943.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3511943/SRX3511943.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3511943/SRX3511943.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 20:07:29: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:07:29: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:07:35: 4000000 INFO @ Sun, 21 Jun 2020 20:07:39: 1000000 INFO @ Sun, 21 Jun 2020 20:07:45: 5000000 INFO @ Sun, 21 Jun 2020 20:07:49: 2000000 INFO @ Sun, 21 Jun 2020 20:07:54: 6000000 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 20:07:58: 3000000 INFO @ Sun, 21 Jun 2020 20:07:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3511943/SRX3511943.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3511943/SRX3511943.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3511943/SRX3511943.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3511943/SRX3511943.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 20:07:59: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:07:59: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:08:04: 7000000 INFO @ Sun, 21 Jun 2020 20:08:08: 4000000 INFO @ Sun, 21 Jun 2020 20:08:09: 1000000 INFO @ Sun, 21 Jun 2020 20:08:15: 8000000 INFO @ Sun, 21 Jun 2020 20:08:18: 2000000 INFO @ Sun, 21 Jun 2020 20:08:19: 5000000 INFO @ Sun, 21 Jun 2020 20:08:25: 9000000 INFO @ Sun, 21 Jun 2020 20:08:26: #1 tag size is determined as 100 bps INFO @ Sun, 21 Jun 2020 20:08:26: #1 tag size = 100 INFO @ Sun, 21 Jun 2020 20:08:26: #1 total tags in treatment: 9131369 INFO @ Sun, 21 Jun 2020 20:08:26: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:08:26: #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 20:08:27: #1 tags after filtering in treatment: 9131354 INFO @ Sun, 21 Jun 2020 20:08:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:08:27: #1 finished! INFO @ Sun, 21 Jun 2020 20:08:27: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:08:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:08:27: 3000000 INFO @ Sun, 21 Jun 2020 20:08:28: #2 number of paired peaks: 468 WARNING @ Sun, 21 Jun 2020 20:08:28: Fewer paired peaks (468) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 468 pairs to build model! INFO @ Sun, 21 Jun 2020 20:08:28: start model_add_line... INFO @ Sun, 21 Jun 2020 20:08:28: start X-correlation... INFO @ Sun, 21 Jun 2020 20:08:28: end of X-cor INFO @ Sun, 21 Jun 2020 20:08:28: #2 finished! INFO @ Sun, 21 Jun 2020 20:08:28: #2 predicted fragment length is 101 bps INFO @ Sun, 21 Jun 2020 20:08:28: #2 alternative fragment length(s) may be 101 bps INFO @ Sun, 21 Jun 2020 20:08:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3511943/SRX3511943.05_model.r WARNING @ Sun, 21 Jun 2020 20:08:28: #2 Since the d (101) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:08:28: #2 You may need to consider one of the other alternative d(s): 101 WARNING @ Sun, 21 Jun 2020 20:08:28: #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 20:08:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:08:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:08:29: 6000000 INFO @ Sun, 21 Jun 2020 20:08:36: 4000000 INFO @ Sun, 21 Jun 2020 20:08:39: 7000000 INFO @ Sun, 21 Jun 2020 20:08:45: 5000000 INFO @ Sun, 21 Jun 2020 20:08:47: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:08:49: 8000000 INFO @ Sun, 21 Jun 2020 20:08:54: 6000000 INFO @ Sun, 21 Jun 2020 20:08:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3511943/SRX3511943.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:08:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3511943/SRX3511943.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:08:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3511943/SRX3511943.05_summits.bed INFO @ Sun, 21 Jun 2020 20:08:56: Done! pass1 - making usageList (613 chroms): 1 millis pass2 - checking and writing primary data (1661 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:08:59: 9000000 INFO @ Sun, 21 Jun 2020 20:09:00: #1 tag size is determined as 100 bps INFO @ Sun, 21 Jun 2020 20:09:00: #1 tag size = 100 INFO @ Sun, 21 Jun 2020 20:09:00: #1 total tags in treatment: 9131369 INFO @ Sun, 21 Jun 2020 20:09:00: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:09:00: #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 20:09:01: #1 tags after filtering in treatment: 9131354 INFO @ Sun, 21 Jun 2020 20:09:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:09:01: #1 finished! INFO @ Sun, 21 Jun 2020 20:09:01: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:09:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:09:01: #2 number of paired peaks: 468 WARNING @ Sun, 21 Jun 2020 20:09:01: Fewer paired peaks (468) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 468 pairs to build model! INFO @ Sun, 21 Jun 2020 20:09:01: start model_add_line... INFO @ Sun, 21 Jun 2020 20:09:01: start X-correlation... INFO @ Sun, 21 Jun 2020 20:09:01: end of X-cor INFO @ Sun, 21 Jun 2020 20:09:01: #2 finished! INFO @ Sun, 21 Jun 2020 20:09:01: #2 predicted fragment length is 101 bps INFO @ Sun, 21 Jun 2020 20:09:01: #2 alternative fragment length(s) may be 101 bps INFO @ Sun, 21 Jun 2020 20:09:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3511943/SRX3511943.10_model.r WARNING @ Sun, 21 Jun 2020 20:09:01: #2 Since the d (101) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:09:01: #2 You may need to consider one of the other alternative d(s): 101 WARNING @ Sun, 21 Jun 2020 20:09:01: #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 20:09:01: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:09:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:09:02: 7000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:09:10: 8000000 INFO @ Sun, 21 Jun 2020 20:09:18: 9000000 INFO @ Sun, 21 Jun 2020 20:09:19: #1 tag size is determined as 100 bps INFO @ Sun, 21 Jun 2020 20:09:19: #1 tag size = 100 INFO @ Sun, 21 Jun 2020 20:09:19: #1 total tags in treatment: 9131369 INFO @ Sun, 21 Jun 2020 20:09:19: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:09:19: #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 20:09:19: #1 tags after filtering in treatment: 9131354 INFO @ Sun, 21 Jun 2020 20:09:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:09:19: #1 finished! INFO @ Sun, 21 Jun 2020 20:09:19: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:09:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:09:20: #2 number of paired peaks: 468 WARNING @ Sun, 21 Jun 2020 20:09:20: Fewer paired peaks (468) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 468 pairs to build model! INFO @ Sun, 21 Jun 2020 20:09:20: start model_add_line... INFO @ Sun, 21 Jun 2020 20:09:20: start X-correlation... INFO @ Sun, 21 Jun 2020 20:09:20: end of X-cor INFO @ Sun, 21 Jun 2020 20:09:20: #2 finished! INFO @ Sun, 21 Jun 2020 20:09:20: #2 predicted fragment length is 101 bps INFO @ Sun, 21 Jun 2020 20:09:20: #2 alternative fragment length(s) may be 101 bps INFO @ Sun, 21 Jun 2020 20:09:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3511943/SRX3511943.20_model.r WARNING @ Sun, 21 Jun 2020 20:09:20: #2 Since the d (101) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:09:20: #2 You may need to consider one of the other alternative d(s): 101 WARNING @ Sun, 21 Jun 2020 20:09:20: #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 20:09:20: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:09:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:09:21: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:09:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3511943/SRX3511943.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:09:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3511943/SRX3511943.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:09:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3511943/SRX3511943.10_summits.bed INFO @ Sun, 21 Jun 2020 20:09:30: Done! pass1 - making usageList (497 chroms): 1 millis pass2 - checking and writing primary data (1047 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:09:40: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:09:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3511943/SRX3511943.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:09:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3511943/SRX3511943.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:09:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3511943/SRX3511943.20_summits.bed INFO @ Sun, 21 Jun 2020 20:09:50: Done! pass1 - making usageList (273 chroms): 1 millis pass2 - checking and writing primary data (437 records, 4 fields): 9 millis CompletedMACS2peakCalling