Job ID = 6627569 SRX = SRX8521405 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-14T03:01:48 prefetch.2.10.7: 1) Downloading 'SRR11978362'... 2020-07-14T03:01:48 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T03:03:41 prefetch.2.10.7: HTTPS download succeed 2020-07-14T03:03:42 prefetch.2.10.7: 'SRR11978362' is valid 2020-07-14T03:03:42 prefetch.2.10.7: 1) 'SRR11978362' was downloaded successfully 2020-07-14T03:03:42 prefetch.2.10.7: 'SRR11978362' has 0 unresolved dependencies Read 12368106 spots for SRR11978362/SRR11978362.sra Written 12368106 spots for SRR11978362/SRR11978362.sra 2020-07-14T03:04:38 prefetch.2.10.7: 1) Downloading 'SRR11978363'... 2020-07-14T03:04:38 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T03:06:10 prefetch.2.10.7: HTTPS download succeed 2020-07-14T03:06:11 prefetch.2.10.7: 'SRR11978363' is valid 2020-07-14T03:06:11 prefetch.2.10.7: 1) 'SRR11978363' was downloaded successfully 2020-07-14T03:06:11 prefetch.2.10.7: 'SRR11978363' has 0 unresolved dependencies Read 12091021 spots for SRR11978363/SRR11978363.sra Written 12091021 spots for SRR11978363/SRR11978363.sra 2020-07-14T03:07:04 prefetch.2.10.7: 1) Downloading 'SRR11978364'... 2020-07-14T03:07:04 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T03:08:36 prefetch.2.10.7: HTTPS download succeed 2020-07-14T03:08:37 prefetch.2.10.7: 'SRR11978364' is valid 2020-07-14T03:08:37 prefetch.2.10.7: 1) 'SRR11978364' was downloaded successfully 2020-07-14T03:08:37 prefetch.2.10.7: 'SRR11978364' has 0 unresolved dependencies Read 12237016 spots for SRR11978364/SRR11978364.sra Written 12237016 spots for SRR11978364/SRR11978364.sra 2020-07-14T03:09:27 prefetch.2.10.7: 1) Downloading 'SRR11978365'... 2020-07-14T03:09:27 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T03:10:42 prefetch.2.10.7: HTTPS download succeed 2020-07-14T03:10:43 prefetch.2.10.7: 'SRR11978365' is valid 2020-07-14T03:10:43 prefetch.2.10.7: 1) 'SRR11978365' was downloaded successfully 2020-07-14T03:10:43 prefetch.2.10.7: 'SRR11978365' has 0 unresolved dependencies Read 12280708 spots for SRR11978365/SRR11978365.sra Written 12280708 spots for SRR11978365/SRR11978365.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627752 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:47 48976851 reads; of these: 48976851 (100.00%) were unpaired; of these: 43682259 (89.19%) aligned 0 times 3992659 (8.15%) aligned exactly 1 time 1301933 (2.66%) aligned >1 times 10.81% overall alignment rate Time searching: 00:06:47 Overall time: 00:06:47 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] 887652 / 5294592 = 0.1677 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 @ Tue, 14 Jul 2020 12:20:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521405/SRX8521405.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521405/SRX8521405.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521405/SRX8521405.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521405/SRX8521405.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 @ Tue, 14 Jul 2020 12:20:27: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:20:27: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:20:33: 1000000 INFO @ Tue, 14 Jul 2020 12:20:39: 2000000 INFO @ Tue, 14 Jul 2020 12:20:45: 3000000 INFO @ Tue, 14 Jul 2020 12:20:51: 4000000 INFO @ Tue, 14 Jul 2020 12:20:53: #1 tag size is determined as 55 bps INFO @ Tue, 14 Jul 2020 12:20:53: #1 tag size = 55 INFO @ Tue, 14 Jul 2020 12:20:53: #1 total tags in treatment: 4406940 INFO @ Tue, 14 Jul 2020 12:20:53: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:20:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 12:20:53: #1 tags after filtering in treatment: 4406940 INFO @ Tue, 14 Jul 2020 12:20:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:20:53: #1 finished! INFO @ Tue, 14 Jul 2020 12:20:53: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:20:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:20:53: #2 number of paired peaks: 478 WARNING @ Tue, 14 Jul 2020 12:20:53: Fewer paired peaks (478) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 478 pairs to build model! INFO @ Tue, 14 Jul 2020 12:20:53: start model_add_line... INFO @ Tue, 14 Jul 2020 12:20:54: start X-correlation... INFO @ Tue, 14 Jul 2020 12:20:54: end of X-cor INFO @ Tue, 14 Jul 2020 12:20:54: #2 finished! INFO @ Tue, 14 Jul 2020 12:20:54: #2 predicted fragment length is 57 bps INFO @ Tue, 14 Jul 2020 12:20:54: #2 alternative fragment length(s) may be 57,527 bps INFO @ Tue, 14 Jul 2020 12:20:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521405/SRX8521405.05_model.r WARNING @ Tue, 14 Jul 2020 12:20:54: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:20:54: #2 You may need to consider one of the other alternative d(s): 57,527 WARNING @ Tue, 14 Jul 2020 12:20:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 12:20:54: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:20:54: #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 @ Tue, 14 Jul 2020 12:20:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521405/SRX8521405.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521405/SRX8521405.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521405/SRX8521405.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521405/SRX8521405.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 @ Tue, 14 Jul 2020 12:20:57: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:20:57: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:21:03: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:21:05: 1000000 INFO @ Tue, 14 Jul 2020 12:21:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521405/SRX8521405.05_peaks.xls INFO @ Tue, 14 Jul 2020 12:21:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521405/SRX8521405.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:21:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521405/SRX8521405.05_summits.bed INFO @ Tue, 14 Jul 2020 12:21:08: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1487 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 12:21:12: 2000000 INFO @ Tue, 14 Jul 2020 12:21:19: 3000000 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 @ Tue, 14 Jul 2020 12:21:27: 4000000 INFO @ Tue, 14 Jul 2020 12:21:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521405/SRX8521405.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521405/SRX8521405.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521405/SRX8521405.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521405/SRX8521405.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 @ Tue, 14 Jul 2020 12:21:27: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:21:27: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:21:30: #1 tag size is determined as 55 bps INFO @ Tue, 14 Jul 2020 12:21:30: #1 tag size = 55 INFO @ Tue, 14 Jul 2020 12:21:30: #1 total tags in treatment: 4406940 INFO @ Tue, 14 Jul 2020 12:21:30: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:21:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 12:21:30: #1 tags after filtering in treatment: 4406940 INFO @ Tue, 14 Jul 2020 12:21:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:21:30: #1 finished! INFO @ Tue, 14 Jul 2020 12:21:30: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:21:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:21:30: #2 number of paired peaks: 478 WARNING @ Tue, 14 Jul 2020 12:21:30: Fewer paired peaks (478) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 478 pairs to build model! INFO @ Tue, 14 Jul 2020 12:21:30: start model_add_line... INFO @ Tue, 14 Jul 2020 12:21:30: start X-correlation... INFO @ Tue, 14 Jul 2020 12:21:30: end of X-cor INFO @ Tue, 14 Jul 2020 12:21:30: #2 finished! INFO @ Tue, 14 Jul 2020 12:21:30: #2 predicted fragment length is 57 bps INFO @ Tue, 14 Jul 2020 12:21:30: #2 alternative fragment length(s) may be 57,527 bps INFO @ Tue, 14 Jul 2020 12:21:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521405/SRX8521405.10_model.r WARNING @ Tue, 14 Jul 2020 12:21:30: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:21:30: #2 You may need to consider one of the other alternative d(s): 57,527 WARNING @ Tue, 14 Jul 2020 12:21:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 12:21:30: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:21:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 12:21:35: 1000000 INFO @ Tue, 14 Jul 2020 12:21:40: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:21:41: 2000000 INFO @ Tue, 14 Jul 2020 12:21:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521405/SRX8521405.10_peaks.xls INFO @ Tue, 14 Jul 2020 12:21:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521405/SRX8521405.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:21:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521405/SRX8521405.10_summits.bed INFO @ Tue, 14 Jul 2020 12:21:44: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (490 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 12:21:48: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 12:21:55: 4000000 INFO @ Tue, 14 Jul 2020 12:21:57: #1 tag size is determined as 55 bps INFO @ Tue, 14 Jul 2020 12:21:57: #1 tag size = 55 INFO @ Tue, 14 Jul 2020 12:21:57: #1 total tags in treatment: 4406940 INFO @ Tue, 14 Jul 2020 12:21:57: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:21:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 12:21:57: #1 tags after filtering in treatment: 4406940 INFO @ Tue, 14 Jul 2020 12:21:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:21:57: #1 finished! INFO @ Tue, 14 Jul 2020 12:21:57: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:21:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:21:58: #2 number of paired peaks: 478 WARNING @ Tue, 14 Jul 2020 12:21:58: Fewer paired peaks (478) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 478 pairs to build model! INFO @ Tue, 14 Jul 2020 12:21:58: start model_add_line... INFO @ Tue, 14 Jul 2020 12:21:58: start X-correlation... INFO @ Tue, 14 Jul 2020 12:21:58: end of X-cor INFO @ Tue, 14 Jul 2020 12:21:58: #2 finished! INFO @ Tue, 14 Jul 2020 12:21:58: #2 predicted fragment length is 57 bps INFO @ Tue, 14 Jul 2020 12:21:58: #2 alternative fragment length(s) may be 57,527 bps INFO @ Tue, 14 Jul 2020 12:21:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521405/SRX8521405.20_model.r WARNING @ Tue, 14 Jul 2020 12:21:58: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:21:58: #2 You may need to consider one of the other alternative d(s): 57,527 WARNING @ Tue, 14 Jul 2020 12:21:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 12:21:58: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:21:58: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 12:22:07: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:22:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521405/SRX8521405.20_peaks.xls INFO @ Tue, 14 Jul 2020 12:22:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521405/SRX8521405.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:22:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521405/SRX8521405.20_summits.bed INFO @ Tue, 14 Jul 2020 12:22:12: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (117 records, 4 fields): 2 millis CompletedMACS2peakCalling