Job ID = 6627298 SRX = SRX8521360 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-14T01:54:59 prefetch.2.10.7: 1) Downloading 'SRR11978094'... 2020-07-14T01:54:59 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:56:30 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:56:31 prefetch.2.10.7: 'SRR11978094' is valid 2020-07-14T01:56:31 prefetch.2.10.7: 1) 'SRR11978094' was downloaded successfully 2020-07-14T01:56:31 prefetch.2.10.7: 'SRR11978094' has 0 unresolved dependencies Read 14659248 spots for SRR11978094/SRR11978094.sra Written 14659248 spots for SRR11978094/SRR11978094.sra 2020-07-14T01:57:34 prefetch.2.10.7: 1) Downloading 'SRR11978095'... 2020-07-14T01:57:34 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:59:09 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:59:09 prefetch.2.10.7: 'SRR11978095' is valid 2020-07-14T01:59:09 prefetch.2.10.7: 1) 'SRR11978095' was downloaded successfully 2020-07-14T01:59:09 prefetch.2.10.7: 'SRR11978095' has 0 unresolved dependencies Read 14243888 spots for SRR11978095/SRR11978095.sra Written 14243888 spots for SRR11978095/SRR11978095.sra 2020-07-14T02:00:10 prefetch.2.10.7: 1) Downloading 'SRR11978096'... 2020-07-14T02:00:10 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:02:30 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:02:30 prefetch.2.10.7: 'SRR11978096' is valid 2020-07-14T02:02:30 prefetch.2.10.7: 1) 'SRR11978096' was downloaded successfully 2020-07-14T02:02:30 prefetch.2.10.7: 'SRR11978096' has 0 unresolved dependencies Read 14833947 spots for SRR11978096/SRR11978096.sra Written 14833947 spots for SRR11978096/SRR11978096.sra 2020-07-14T02:03:36 prefetch.2.10.7: 1) Downloading 'SRR11978097'... 2020-07-14T02:03:36 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:07:49 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:07:50 prefetch.2.10.7: 'SRR11978097' is valid 2020-07-14T02:07:50 prefetch.2.10.7: 1) 'SRR11978097' was downloaded successfully 2020-07-14T02:07:50 prefetch.2.10.7: 'SRR11978097' has 0 unresolved dependencies Read 14667689 spots for SRR11978097/SRR11978097.sra Written 14667689 spots for SRR11978097/SRR11978097.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627552 ("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: 00:08:36 58404772 reads; of these: 58404772 (100.00%) were unpaired; of these: 49393821 (84.57%) aligned 0 times 6790028 (11.63%) aligned exactly 1 time 2220923 (3.80%) aligned >1 times 15.43% overall alignment rate Time searching: 00:08:36 Overall time: 00:08:36 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] 1861788 / 9010951 = 0.2066 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 11:20:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521360/SRX8521360.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521360/SRX8521360.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521360/SRX8521360.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521360/SRX8521360.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 11:20:33: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:20:33: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:20:39: 1000000 INFO @ Tue, 14 Jul 2020 11:20:45: 2000000 INFO @ Tue, 14 Jul 2020 11:20:50: 3000000 INFO @ Tue, 14 Jul 2020 11:20:56: 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 11:21:02: 5000000 INFO @ Tue, 14 Jul 2020 11:21:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521360/SRX8521360.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521360/SRX8521360.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521360/SRX8521360.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521360/SRX8521360.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 11:21:03: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:21:03: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:21:09: 6000000 INFO @ Tue, 14 Jul 2020 11:21:10: 1000000 INFO @ Tue, 14 Jul 2020 11:21:16: 7000000 INFO @ Tue, 14 Jul 2020 11:21:17: #1 tag size is determined as 63 bps INFO @ Tue, 14 Jul 2020 11:21:17: #1 tag size = 63 INFO @ Tue, 14 Jul 2020 11:21:17: #1 total tags in treatment: 7149163 INFO @ Tue, 14 Jul 2020 11:21:17: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:21:17: #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 11:21:17: #1 tags after filtering in treatment: 7149163 INFO @ Tue, 14 Jul 2020 11:21:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:21:17: #1 finished! INFO @ Tue, 14 Jul 2020 11:21:17: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:21:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:21:17: #2 number of paired peaks: 416 WARNING @ Tue, 14 Jul 2020 11:21:17: Fewer paired peaks (416) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 416 pairs to build model! INFO @ Tue, 14 Jul 2020 11:21:17: start model_add_line... INFO @ Tue, 14 Jul 2020 11:21:17: start X-correlation... INFO @ Tue, 14 Jul 2020 11:21:17: end of X-cor INFO @ Tue, 14 Jul 2020 11:21:17: #2 finished! INFO @ Tue, 14 Jul 2020 11:21:17: #2 predicted fragment length is 63 bps INFO @ Tue, 14 Jul 2020 11:21:17: #2 alternative fragment length(s) may be 63 bps INFO @ Tue, 14 Jul 2020 11:21:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521360/SRX8521360.05_model.r WARNING @ Tue, 14 Jul 2020 11:21:17: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:21:17: #2 You may need to consider one of the other alternative d(s): 63 WARNING @ Tue, 14 Jul 2020 11:21:17: #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 11:21:17: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:21:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:21:18: 2000000 INFO @ Tue, 14 Jul 2020 11:21:25: 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 11:21:32: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:21:32: 4000000 INFO @ Tue, 14 Jul 2020 11:21:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521360/SRX8521360.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521360/SRX8521360.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521360/SRX8521360.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521360/SRX8521360.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 11:21:33: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:21:33: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:21:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521360/SRX8521360.05_peaks.xls INFO @ Tue, 14 Jul 2020 11:21:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521360/SRX8521360.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:21:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521360/SRX8521360.05_summits.bed INFO @ Tue, 14 Jul 2020 11:21:39: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3241 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 11:21:40: 5000000 INFO @ Tue, 14 Jul 2020 11:21:40: 1000000 INFO @ Tue, 14 Jul 2020 11:21:47: 6000000 INFO @ Tue, 14 Jul 2020 11:21:47: 2000000 INFO @ Tue, 14 Jul 2020 11:21:54: 7000000 INFO @ Tue, 14 Jul 2020 11:21:55: 3000000 INFO @ Tue, 14 Jul 2020 11:21:55: #1 tag size is determined as 63 bps INFO @ Tue, 14 Jul 2020 11:21:55: #1 tag size = 63 INFO @ Tue, 14 Jul 2020 11:21:55: #1 total tags in treatment: 7149163 INFO @ Tue, 14 Jul 2020 11:21:55: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:21:55: #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 11:21:55: #1 tags after filtering in treatment: 7149163 INFO @ Tue, 14 Jul 2020 11:21:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:21:55: #1 finished! INFO @ Tue, 14 Jul 2020 11:21:55: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:21:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:21:56: #2 number of paired peaks: 416 WARNING @ Tue, 14 Jul 2020 11:21:56: Fewer paired peaks (416) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 416 pairs to build model! INFO @ Tue, 14 Jul 2020 11:21:56: start model_add_line... INFO @ Tue, 14 Jul 2020 11:21:56: start X-correlation... INFO @ Tue, 14 Jul 2020 11:21:56: end of X-cor INFO @ Tue, 14 Jul 2020 11:21:56: #2 finished! INFO @ Tue, 14 Jul 2020 11:21:56: #2 predicted fragment length is 63 bps INFO @ Tue, 14 Jul 2020 11:21:56: #2 alternative fragment length(s) may be 63 bps INFO @ Tue, 14 Jul 2020 11:21:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521360/SRX8521360.10_model.r WARNING @ Tue, 14 Jul 2020 11:21:56: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:21:56: #2 You may need to consider one of the other alternative d(s): 63 WARNING @ Tue, 14 Jul 2020 11:21:56: #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 11:21:56: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:21:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:22:02: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 11:22:09: 5000000 INFO @ Tue, 14 Jul 2020 11:22:11: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:22:16: 6000000 INFO @ Tue, 14 Jul 2020 11:22:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521360/SRX8521360.10_peaks.xls INFO @ Tue, 14 Jul 2020 11:22:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521360/SRX8521360.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:22:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521360/SRX8521360.10_summits.bed INFO @ Tue, 14 Jul 2020 11:22:18: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1263 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 11:22:23: 7000000 INFO @ Tue, 14 Jul 2020 11:22:24: #1 tag size is determined as 63 bps INFO @ Tue, 14 Jul 2020 11:22:24: #1 tag size = 63 INFO @ Tue, 14 Jul 2020 11:22:24: #1 total tags in treatment: 7149163 INFO @ Tue, 14 Jul 2020 11:22:24: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:22:24: #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 11:22:24: #1 tags after filtering in treatment: 7149163 INFO @ Tue, 14 Jul 2020 11:22:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:22:24: #1 finished! INFO @ Tue, 14 Jul 2020 11:22:24: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:22:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:22:24: #2 number of paired peaks: 416 WARNING @ Tue, 14 Jul 2020 11:22:24: Fewer paired peaks (416) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 416 pairs to build model! INFO @ Tue, 14 Jul 2020 11:22:24: start model_add_line... INFO @ Tue, 14 Jul 2020 11:22:24: start X-correlation... INFO @ Tue, 14 Jul 2020 11:22:24: end of X-cor INFO @ Tue, 14 Jul 2020 11:22:24: #2 finished! INFO @ Tue, 14 Jul 2020 11:22:24: #2 predicted fragment length is 63 bps INFO @ Tue, 14 Jul 2020 11:22:24: #2 alternative fragment length(s) may be 63 bps INFO @ Tue, 14 Jul 2020 11:22:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521360/SRX8521360.20_model.r WARNING @ Tue, 14 Jul 2020 11:22:24: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:22:24: #2 You may need to consider one of the other alternative d(s): 63 WARNING @ Tue, 14 Jul 2020 11:22:24: #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 11:22:24: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:22:24: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 11:22:39: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:22:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521360/SRX8521360.20_peaks.xls INFO @ Tue, 14 Jul 2020 11:22:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521360/SRX8521360.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:22:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521360/SRX8521360.20_summits.bed INFO @ Tue, 14 Jul 2020 11:22:46: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (301 records, 4 fields): 2 millis CompletedMACS2peakCalling