Job ID = 6498705 SRX = SRX706816 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T23:52:06 prefetch.2.10.7: 1) Downloading 'SRR1581497'... 2020-06-25T23:52:07 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T23:54:45 prefetch.2.10.7: HTTPS download succeed 2020-06-25T23:54:45 prefetch.2.10.7: 1) 'SRR1581497' was downloaded successfully Read 28448833 spots for SRR1581497/SRR1581497.sra Written 28448833 spots for SRR1581497/SRR1581497.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: 00:04:56 28448833 reads; of these: 28448833 (100.00%) were unpaired; of these: 21644818 (76.08%) aligned 0 times 5158861 (18.13%) aligned exactly 1 time 1645154 (5.78%) aligned >1 times 23.92% overall alignment rate Time searching: 00:04:56 Overall time: 00:04:56 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_rmdupse_core] 4192073 / 6804015 = 0.6161 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 09:03:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX706816/SRX706816.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX706816/SRX706816.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX706816/SRX706816.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX706816/SRX706816.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 09:03:04: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:03:04: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:03:10: 1000000 INFO @ Fri, 26 Jun 2020 09:03:17: 2000000 INFO @ Fri, 26 Jun 2020 09:03:21: #1 tag size is determined as 44 bps INFO @ Fri, 26 Jun 2020 09:03:21: #1 tag size = 44 INFO @ Fri, 26 Jun 2020 09:03:21: #1 total tags in treatment: 2611942 INFO @ Fri, 26 Jun 2020 09:03:21: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:03:21: #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 09:03:21: #1 tags after filtering in treatment: 2611942 INFO @ Fri, 26 Jun 2020 09:03:21: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:03:21: #1 finished! INFO @ Fri, 26 Jun 2020 09:03:21: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:03:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:03:21: #2 number of paired peaks: 422 WARNING @ Fri, 26 Jun 2020 09:03:21: Fewer paired peaks (422) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 422 pairs to build model! INFO @ Fri, 26 Jun 2020 09:03:21: start model_add_line... INFO @ Fri, 26 Jun 2020 09:03:21: start X-correlation... INFO @ Fri, 26 Jun 2020 09:03:21: end of X-cor INFO @ Fri, 26 Jun 2020 09:03:21: #2 finished! INFO @ Fri, 26 Jun 2020 09:03:21: #2 predicted fragment length is 45 bps INFO @ Fri, 26 Jun 2020 09:03:21: #2 alternative fragment length(s) may be 45 bps INFO @ Fri, 26 Jun 2020 09:03:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX706816/SRX706816.05_model.r WARNING @ Fri, 26 Jun 2020 09:03:21: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:03:21: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Fri, 26 Jun 2020 09:03:21: #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 09:03:21: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:03:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:03:28: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:03:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX706816/SRX706816.05_peaks.xls INFO @ Fri, 26 Jun 2020 09:03:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX706816/SRX706816.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:03:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX706816/SRX706816.05_summits.bed INFO @ Fri, 26 Jun 2020 09:03:31: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (876 records, 4 fields): 3 millis CompletedMACS2peakCalling 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 09:03:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX706816/SRX706816.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX706816/SRX706816.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX706816/SRX706816.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX706816/SRX706816.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 09:03:34: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:03:34: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:03:40: 1000000 INFO @ Fri, 26 Jun 2020 09:03:47: 2000000 INFO @ Fri, 26 Jun 2020 09:03:51: #1 tag size is determined as 44 bps INFO @ Fri, 26 Jun 2020 09:03:51: #1 tag size = 44 INFO @ Fri, 26 Jun 2020 09:03:51: #1 total tags in treatment: 2611942 INFO @ Fri, 26 Jun 2020 09:03:51: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:03:51: #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 09:03:51: #1 tags after filtering in treatment: 2611942 INFO @ Fri, 26 Jun 2020 09:03:51: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:03:51: #1 finished! INFO @ Fri, 26 Jun 2020 09:03:51: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:03:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:03:51: #2 number of paired peaks: 422 WARNING @ Fri, 26 Jun 2020 09:03:51: Fewer paired peaks (422) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 422 pairs to build model! INFO @ Fri, 26 Jun 2020 09:03:51: start model_add_line... INFO @ Fri, 26 Jun 2020 09:03:51: start X-correlation... INFO @ Fri, 26 Jun 2020 09:03:51: end of X-cor INFO @ Fri, 26 Jun 2020 09:03:51: #2 finished! INFO @ Fri, 26 Jun 2020 09:03:51: #2 predicted fragment length is 45 bps INFO @ Fri, 26 Jun 2020 09:03:51: #2 alternative fragment length(s) may be 45 bps INFO @ Fri, 26 Jun 2020 09:03:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX706816/SRX706816.10_model.r WARNING @ Fri, 26 Jun 2020 09:03:51: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:03:51: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Fri, 26 Jun 2020 09:03:51: #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 09:03:51: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:03:51: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:03:58: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:04:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX706816/SRX706816.10_peaks.xls INFO @ Fri, 26 Jun 2020 09:04:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX706816/SRX706816.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:04:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX706816/SRX706816.10_summits.bed INFO @ Fri, 26 Jun 2020 09:04:01: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (375 records, 4 fields): 2 millis CompletedMACS2peakCalling 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 09:04:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX706816/SRX706816.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX706816/SRX706816.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX706816/SRX706816.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX706816/SRX706816.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 09:04:04: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:04:04: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:04:10: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 09:04:17: 2000000 INFO @ Fri, 26 Jun 2020 09:04:20: #1 tag size is determined as 44 bps INFO @ Fri, 26 Jun 2020 09:04:20: #1 tag size = 44 INFO @ Fri, 26 Jun 2020 09:04:20: #1 total tags in treatment: 2611942 INFO @ Fri, 26 Jun 2020 09:04:20: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:04:20: #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 09:04:20: #1 tags after filtering in treatment: 2611942 INFO @ Fri, 26 Jun 2020 09:04:20: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:04:20: #1 finished! INFO @ Fri, 26 Jun 2020 09:04:20: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:04:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:04:21: #2 number of paired peaks: 422 WARNING @ Fri, 26 Jun 2020 09:04:21: Fewer paired peaks (422) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 422 pairs to build model! INFO @ Fri, 26 Jun 2020 09:04:21: start model_add_line... INFO @ Fri, 26 Jun 2020 09:04:21: start X-correlation... INFO @ Fri, 26 Jun 2020 09:04:21: end of X-cor INFO @ Fri, 26 Jun 2020 09:04:21: #2 finished! INFO @ Fri, 26 Jun 2020 09:04:21: #2 predicted fragment length is 45 bps INFO @ Fri, 26 Jun 2020 09:04:21: #2 alternative fragment length(s) may be 45 bps INFO @ Fri, 26 Jun 2020 09:04:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX706816/SRX706816.20_model.r WARNING @ Fri, 26 Jun 2020 09:04:21: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:04:21: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Fri, 26 Jun 2020 09:04:21: #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 09:04:21: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:04:21: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 09:04:27: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:04:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX706816/SRX706816.20_peaks.xls INFO @ Fri, 26 Jun 2020 09:04:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX706816/SRX706816.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:04:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX706816/SRX706816.20_summits.bed INFO @ Fri, 26 Jun 2020 09:04:30: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (195 records, 4 fields): 2 millis CompletedMACS2peakCalling