Job ID = 6627581 SRX = SRX8521414 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-14T03:04:41 prefetch.2.10.7: 1) Downloading 'SRR11978398'... 2020-07-14T03:04:41 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T03:06:04 prefetch.2.10.7: HTTPS download succeed 2020-07-14T03:06:04 prefetch.2.10.7: 'SRR11978398' is valid 2020-07-14T03:06:04 prefetch.2.10.7: 1) 'SRR11978398' was downloaded successfully 2020-07-14T03:06:04 prefetch.2.10.7: 'SRR11978398' has 0 unresolved dependencies Read 12915326 spots for SRR11978398/SRR11978398.sra Written 12915326 spots for SRR11978398/SRR11978398.sra 2020-07-14T03:07:03 prefetch.2.10.7: 1) Downloading 'SRR11978399'... 2020-07-14T03:07:03 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T03:08:20 prefetch.2.10.7: HTTPS download succeed 2020-07-14T03:08:21 prefetch.2.10.7: 'SRR11978399' is valid 2020-07-14T03:08:21 prefetch.2.10.7: 1) 'SRR11978399' was downloaded successfully 2020-07-14T03:08:21 prefetch.2.10.7: 'SRR11978399' has 0 unresolved dependencies Read 12677822 spots for SRR11978399/SRR11978399.sra Written 12677822 spots for SRR11978399/SRR11978399.sra 2020-07-14T03:09:17 prefetch.2.10.7: 1) Downloading 'SRR11978400'... 2020-07-14T03:09:17 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T03:11:17 prefetch.2.10.7: HTTPS download succeed 2020-07-14T03:11:17 prefetch.2.10.7: 'SRR11978400' is valid 2020-07-14T03:11:17 prefetch.2.10.7: 1) 'SRR11978400' was downloaded successfully 2020-07-14T03:11:17 prefetch.2.10.7: 'SRR11978400' has 0 unresolved dependencies Read 12891972 spots for SRR11978400/SRR11978400.sra Written 12891972 spots for SRR11978400/SRR11978400.sra 2020-07-14T03:12:15 prefetch.2.10.7: 1) Downloading 'SRR11978401'... 2020-07-14T03:12:15 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T03:13:23 prefetch.2.10.7: HTTPS download succeed 2020-07-14T03:13:24 prefetch.2.10.7: 'SRR11978401' is valid 2020-07-14T03:13:24 prefetch.2.10.7: 1) 'SRR11978401' was downloaded successfully 2020-07-14T03:13:24 prefetch.2.10.7: 'SRR11978401' has 0 unresolved dependencies Read 12749129 spots for SRR11978401/SRR11978401.sra Written 12749129 spots for SRR11978401/SRR11978401.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627767 ("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 51234249 reads; of these: 51234249 (100.00%) were unpaired; of these: 47688442 (93.08%) aligned 0 times 2654405 (5.18%) aligned exactly 1 time 891402 (1.74%) aligned >1 times 6.92% 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] 733281 / 3545807 = 0.2068 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 12:22:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521414/SRX8521414.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521414/SRX8521414.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521414/SRX8521414.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521414/SRX8521414.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 12:22:38: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:22:38: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:22:44: 1000000 INFO @ Tue, 14 Jul 2020 12:22:50: 2000000 INFO @ Tue, 14 Jul 2020 12:22:54: #1 tag size is determined as 63 bps INFO @ Tue, 14 Jul 2020 12:22:54: #1 tag size = 63 INFO @ Tue, 14 Jul 2020 12:22:54: #1 total tags in treatment: 2812526 INFO @ Tue, 14 Jul 2020 12:22:54: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:22:54: #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 12:22:54: #1 tags after filtering in treatment: 2812526 INFO @ Tue, 14 Jul 2020 12:22:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:22:54: #1 finished! INFO @ Tue, 14 Jul 2020 12:22:54: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:22:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:22:55: #2 number of paired peaks: 711 WARNING @ Tue, 14 Jul 2020 12:22:55: Fewer paired peaks (711) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 711 pairs to build model! INFO @ Tue, 14 Jul 2020 12:22:55: start model_add_line... INFO @ Tue, 14 Jul 2020 12:22:55: start X-correlation... INFO @ Tue, 14 Jul 2020 12:22:55: end of X-cor INFO @ Tue, 14 Jul 2020 12:22:55: #2 finished! INFO @ Tue, 14 Jul 2020 12:22:55: #2 predicted fragment length is 59 bps INFO @ Tue, 14 Jul 2020 12:22:55: #2 alternative fragment length(s) may be 59 bps INFO @ Tue, 14 Jul 2020 12:22:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521414/SRX8521414.05_model.r WARNING @ Tue, 14 Jul 2020 12:22:55: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:22:55: #2 You may need to consider one of the other alternative d(s): 59 WARNING @ Tue, 14 Jul 2020 12:22:55: #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 12:22:55: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:22:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 12:23:00: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:23:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521414/SRX8521414.05_peaks.xls INFO @ Tue, 14 Jul 2020 12:23:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521414/SRX8521414.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:23:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521414/SRX8521414.05_summits.bed INFO @ Tue, 14 Jul 2020 12:23:04: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (1275 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 @ Tue, 14 Jul 2020 12:23:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521414/SRX8521414.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521414/SRX8521414.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521414/SRX8521414.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521414/SRX8521414.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 12:23:08: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:23:08: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:23:14: 1000000 INFO @ Tue, 14 Jul 2020 12:23:20: 2000000 INFO @ Tue, 14 Jul 2020 12:23:24: #1 tag size is determined as 63 bps INFO @ Tue, 14 Jul 2020 12:23:24: #1 tag size = 63 INFO @ Tue, 14 Jul 2020 12:23:24: #1 total tags in treatment: 2812526 INFO @ Tue, 14 Jul 2020 12:23:24: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:23:24: #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 12:23:24: #1 tags after filtering in treatment: 2812526 INFO @ Tue, 14 Jul 2020 12:23:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:23:24: #1 finished! INFO @ Tue, 14 Jul 2020 12:23:24: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:23:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:23:25: #2 number of paired peaks: 711 WARNING @ Tue, 14 Jul 2020 12:23:25: Fewer paired peaks (711) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 711 pairs to build model! INFO @ Tue, 14 Jul 2020 12:23:25: start model_add_line... INFO @ Tue, 14 Jul 2020 12:23:25: start X-correlation... INFO @ Tue, 14 Jul 2020 12:23:25: end of X-cor INFO @ Tue, 14 Jul 2020 12:23:25: #2 finished! INFO @ Tue, 14 Jul 2020 12:23:25: #2 predicted fragment length is 59 bps INFO @ Tue, 14 Jul 2020 12:23:25: #2 alternative fragment length(s) may be 59 bps INFO @ Tue, 14 Jul 2020 12:23:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521414/SRX8521414.10_model.r WARNING @ Tue, 14 Jul 2020 12:23:25: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:23:25: #2 You may need to consider one of the other alternative d(s): 59 WARNING @ Tue, 14 Jul 2020 12:23:25: #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 12:23:25: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:23:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 12:23:31: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:23:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521414/SRX8521414.10_peaks.xls INFO @ Tue, 14 Jul 2020 12:23:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521414/SRX8521414.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:23:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521414/SRX8521414.10_summits.bed INFO @ Tue, 14 Jul 2020 12:23:34: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (567 records, 4 fields): 1 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 @ Tue, 14 Jul 2020 12:23:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521414/SRX8521414.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521414/SRX8521414.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521414/SRX8521414.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521414/SRX8521414.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 12:23:38: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:23:38: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:23:44: 1000000 INFO @ Tue, 14 Jul 2020 12:23:50: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 12:23:55: #1 tag size is determined as 63 bps INFO @ Tue, 14 Jul 2020 12:23:55: #1 tag size = 63 INFO @ Tue, 14 Jul 2020 12:23:55: #1 total tags in treatment: 2812526 INFO @ Tue, 14 Jul 2020 12:23:55: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:23:55: #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 12:23:55: #1 tags after filtering in treatment: 2812526 INFO @ Tue, 14 Jul 2020 12:23:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:23:55: #1 finished! INFO @ Tue, 14 Jul 2020 12:23:55: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:23:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:23:55: #2 number of paired peaks: 711 WARNING @ Tue, 14 Jul 2020 12:23:55: Fewer paired peaks (711) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 711 pairs to build model! INFO @ Tue, 14 Jul 2020 12:23:55: start model_add_line... INFO @ Tue, 14 Jul 2020 12:23:55: start X-correlation... INFO @ Tue, 14 Jul 2020 12:23:55: end of X-cor INFO @ Tue, 14 Jul 2020 12:23:55: #2 finished! INFO @ Tue, 14 Jul 2020 12:23:55: #2 predicted fragment length is 59 bps INFO @ Tue, 14 Jul 2020 12:23:55: #2 alternative fragment length(s) may be 59 bps INFO @ Tue, 14 Jul 2020 12:23:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521414/SRX8521414.20_model.r WARNING @ Tue, 14 Jul 2020 12:23:55: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:23:55: #2 You may need to consider one of the other alternative d(s): 59 WARNING @ Tue, 14 Jul 2020 12:23:55: #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 12:23:55: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:23:55: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 12:24:01: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:24:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521414/SRX8521414.20_peaks.xls INFO @ Tue, 14 Jul 2020 12:24:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521414/SRX8521414.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:24:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521414/SRX8521414.20_summits.bed INFO @ Tue, 14 Jul 2020 12:24:04: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (115 records, 4 fields): 2 millis CompletedMACS2peakCalling