Job ID = 6627175 SRX = SRX8521306 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-14T01:26:27 prefetch.2.10.7: 1) Downloading 'SRR11978673'... 2020-07-14T01:26:27 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:28:17 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:28:18 prefetch.2.10.7: 'SRR11978673' is valid 2020-07-14T01:28:18 prefetch.2.10.7: 1) 'SRR11978673' was downloaded successfully 2020-07-14T01:28:18 prefetch.2.10.7: 'SRR11978673' has 0 unresolved dependencies Read 14131999 spots for SRR11978673/SRR11978673.sra Written 14131999 spots for SRR11978673/SRR11978673.sra 2020-07-14T01:29:15 prefetch.2.10.7: 1) Downloading 'SRR11978674'... 2020-07-14T01:29:15 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:31:07 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:31:08 prefetch.2.10.7: 'SRR11978674' is valid 2020-07-14T01:31:08 prefetch.2.10.7: 1) 'SRR11978674' was downloaded successfully 2020-07-14T01:31:08 prefetch.2.10.7: 'SRR11978674' has 0 unresolved dependencies Read 14105023 spots for SRR11978674/SRR11978674.sra Written 14105023 spots for SRR11978674/SRR11978674.sra 2020-07-14T01:32:09 prefetch.2.10.7: 1) Downloading 'SRR11978675'... 2020-07-14T01:32:09 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:34:01 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:34:01 prefetch.2.10.7: 'SRR11978675' is valid 2020-07-14T01:34:01 prefetch.2.10.7: 1) 'SRR11978675' was downloaded successfully 2020-07-14T01:34:01 prefetch.2.10.7: 'SRR11978675' has 0 unresolved dependencies Read 14019939 spots for SRR11978675/SRR11978675.sra Written 14019939 spots for SRR11978675/SRR11978675.sra 2020-07-14T01:35:02 prefetch.2.10.7: 1) Downloading 'SRR11978676'... 2020-07-14T01:35:02 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:36:51 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:36:52 prefetch.2.10.7: 'SRR11978676' is valid 2020-07-14T01:36:52 prefetch.2.10.7: 1) 'SRR11978676' was downloaded successfully 2020-07-14T01:36:52 prefetch.2.10.7: 'SRR11978676' has 0 unresolved dependencies Read 14211451 spots for SRR11978676/SRR11978676.sra Written 14211451 spots for SRR11978676/SRR11978676.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627444 ("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: 00:10:58 56468412 reads; of these: 56468412 (100.00%) were unpaired; of these: 46219469 (81.85%) aligned 0 times 6953974 (12.31%) aligned exactly 1 time 3294969 (5.84%) aligned >1 times 18.15% overall alignment rate Time searching: 00:10:58 Overall time: 00:10:58 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_sort_core] merging from 8 files... [bam_rmdupse_core] 2172181 / 10248943 = 0.2119 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 10:52:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521306/SRX8521306.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521306/SRX8521306.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521306/SRX8521306.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521306/SRX8521306.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 10:52:12: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:52:12: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:52:18: 1000000 INFO @ Tue, 14 Jul 2020 10:52:24: 2000000 INFO @ Tue, 14 Jul 2020 10:52:30: 3000000 INFO @ Tue, 14 Jul 2020 10:52:36: 4000000 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 10:52:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521306/SRX8521306.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521306/SRX8521306.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521306/SRX8521306.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521306/SRX8521306.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 10:52:42: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:52:42: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:52:43: 5000000 INFO @ Tue, 14 Jul 2020 10:52:49: 1000000 INFO @ Tue, 14 Jul 2020 10:52:50: 6000000 INFO @ Tue, 14 Jul 2020 10:52:56: 2000000 INFO @ Tue, 14 Jul 2020 10:52:57: 7000000 INFO @ Tue, 14 Jul 2020 10:53:03: 3000000 INFO @ Tue, 14 Jul 2020 10:53:04: 8000000 INFO @ Tue, 14 Jul 2020 10:53:04: #1 tag size is determined as 67 bps INFO @ Tue, 14 Jul 2020 10:53:04: #1 tag size = 67 INFO @ Tue, 14 Jul 2020 10:53:04: #1 total tags in treatment: 8076762 INFO @ Tue, 14 Jul 2020 10:53:04: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:53:04: #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 10:53:04: #1 tags after filtering in treatment: 8076762 INFO @ Tue, 14 Jul 2020 10:53:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:53:04: #1 finished! INFO @ Tue, 14 Jul 2020 10:53:04: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:53:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:53:05: #2 number of paired peaks: 186 WARNING @ Tue, 14 Jul 2020 10:53:05: Fewer paired peaks (186) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 186 pairs to build model! INFO @ Tue, 14 Jul 2020 10:53:05: start model_add_line... INFO @ Tue, 14 Jul 2020 10:53:05: start X-correlation... INFO @ Tue, 14 Jul 2020 10:53:05: end of X-cor INFO @ Tue, 14 Jul 2020 10:53:05: #2 finished! INFO @ Tue, 14 Jul 2020 10:53:05: #2 predicted fragment length is 57 bps INFO @ Tue, 14 Jul 2020 10:53:05: #2 alternative fragment length(s) may be 57 bps INFO @ Tue, 14 Jul 2020 10:53:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521306/SRX8521306.05_model.r WARNING @ Tue, 14 Jul 2020 10:53:05: #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 10:53:05: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Tue, 14 Jul 2020 10:53:05: #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 10:53:05: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:53:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:53:09: 4000000 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 10:53:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521306/SRX8521306.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521306/SRX8521306.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521306/SRX8521306.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521306/SRX8521306.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 10:53:12: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:53:12: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:53:16: 5000000 INFO @ Tue, 14 Jul 2020 10:53:20: 1000000 INFO @ Tue, 14 Jul 2020 10:53:20: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:53:23: 6000000 INFO @ Tue, 14 Jul 2020 10:53:27: 2000000 INFO @ Tue, 14 Jul 2020 10:53:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521306/SRX8521306.05_peaks.xls INFO @ Tue, 14 Jul 2020 10:53:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521306/SRX8521306.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:53:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521306/SRX8521306.05_summits.bed INFO @ Tue, 14 Jul 2020 10:53:29: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1672 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:53:30: 7000000 INFO @ Tue, 14 Jul 2020 10:53:35: 3000000 INFO @ Tue, 14 Jul 2020 10:53:38: 8000000 INFO @ Tue, 14 Jul 2020 10:53:38: #1 tag size is determined as 67 bps INFO @ Tue, 14 Jul 2020 10:53:38: #1 tag size = 67 INFO @ Tue, 14 Jul 2020 10:53:38: #1 total tags in treatment: 8076762 INFO @ Tue, 14 Jul 2020 10:53:38: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:53:38: #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 10:53:38: #1 tags after filtering in treatment: 8076762 INFO @ Tue, 14 Jul 2020 10:53:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:53:38: #1 finished! INFO @ Tue, 14 Jul 2020 10:53:38: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:53:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:53:39: #2 number of paired peaks: 186 WARNING @ Tue, 14 Jul 2020 10:53:39: Fewer paired peaks (186) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 186 pairs to build model! INFO @ Tue, 14 Jul 2020 10:53:39: start model_add_line... INFO @ Tue, 14 Jul 2020 10:53:39: start X-correlation... INFO @ Tue, 14 Jul 2020 10:53:39: end of X-cor INFO @ Tue, 14 Jul 2020 10:53:39: #2 finished! INFO @ Tue, 14 Jul 2020 10:53:39: #2 predicted fragment length is 57 bps INFO @ Tue, 14 Jul 2020 10:53:39: #2 alternative fragment length(s) may be 57 bps INFO @ Tue, 14 Jul 2020 10:53:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521306/SRX8521306.10_model.r WARNING @ Tue, 14 Jul 2020 10:53:39: #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 10:53:39: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Tue, 14 Jul 2020 10:53:39: #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 10:53:39: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:53:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:53:42: 4000000 INFO @ Tue, 14 Jul 2020 10:53:50: 5000000 INFO @ Tue, 14 Jul 2020 10:53:54: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:53:56: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 10:54:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521306/SRX8521306.10_peaks.xls INFO @ Tue, 14 Jul 2020 10:54:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521306/SRX8521306.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:54:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521306/SRX8521306.10_summits.bed INFO @ Tue, 14 Jul 2020 10:54:03: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (915 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:54:03: 7000000 INFO @ Tue, 14 Jul 2020 10:54:10: 8000000 INFO @ Tue, 14 Jul 2020 10:54:11: #1 tag size is determined as 67 bps INFO @ Tue, 14 Jul 2020 10:54:11: #1 tag size = 67 INFO @ Tue, 14 Jul 2020 10:54:11: #1 total tags in treatment: 8076762 INFO @ Tue, 14 Jul 2020 10:54:11: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:54:11: #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 10:54:11: #1 tags after filtering in treatment: 8076762 INFO @ Tue, 14 Jul 2020 10:54:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:54:11: #1 finished! INFO @ Tue, 14 Jul 2020 10:54:11: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:54:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:54:11: #2 number of paired peaks: 186 WARNING @ Tue, 14 Jul 2020 10:54:11: Fewer paired peaks (186) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 186 pairs to build model! INFO @ Tue, 14 Jul 2020 10:54:11: start model_add_line... INFO @ Tue, 14 Jul 2020 10:54:11: start X-correlation... INFO @ Tue, 14 Jul 2020 10:54:11: end of X-cor INFO @ Tue, 14 Jul 2020 10:54:11: #2 finished! INFO @ Tue, 14 Jul 2020 10:54:11: #2 predicted fragment length is 57 bps INFO @ Tue, 14 Jul 2020 10:54:11: #2 alternative fragment length(s) may be 57 bps INFO @ Tue, 14 Jul 2020 10:54:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521306/SRX8521306.20_model.r WARNING @ Tue, 14 Jul 2020 10:54:11: #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 10:54:11: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Tue, 14 Jul 2020 10:54:11: #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 10:54:11: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:54:11: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 10:54:27: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:54:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521306/SRX8521306.20_peaks.xls INFO @ Tue, 14 Jul 2020 10:54:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521306/SRX8521306.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:54:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521306/SRX8521306.20_summits.bed INFO @ Tue, 14 Jul 2020 10:54:35: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (390 records, 4 fields): 2 millis CompletedMACS2peakCalling