Job ID = 6627102 SRX = SRX8521285 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-14T00:54:05 prefetch.2.10.7: 1) Downloading 'SRR11978430'... 2020-07-14T00:54:05 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T00:57:19 prefetch.2.10.7: HTTPS download succeed 2020-07-14T00:57:19 prefetch.2.10.7: 1) 'SRR11978430' was downloaded successfully 2020-07-14T00:57:19 prefetch.2.10.7: 'SRR11978430' has 0 unresolved dependencies Read 18714040 spots for SRR11978430/SRR11978430.sra Written 18714040 spots for SRR11978430/SRR11978430.sra 2020-07-14T00:58:33 prefetch.2.10.7: 1) Downloading 'SRR11978431'... 2020-07-14T00:58:33 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:01:26 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:01:26 prefetch.2.10.7: 1) 'SRR11978431' was downloaded successfully 2020-07-14T01:01:26 prefetch.2.10.7: 'SRR11978431' has 0 unresolved dependencies Read 18735233 spots for SRR11978431/SRR11978431.sra Written 18735233 spots for SRR11978431/SRR11978431.sra 2020-07-14T01:02:40 prefetch.2.10.7: 1) Downloading 'SRR11978432'... 2020-07-14T01:02:40 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:04:17 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:04:17 prefetch.2.10.7: 1) 'SRR11978432' was downloaded successfully 2020-07-14T01:04:17 prefetch.2.10.7: 'SRR11978432' has 0 unresolved dependencies Read 19345046 spots for SRR11978432/SRR11978432.sra Written 19345046 spots for SRR11978432/SRR11978432.sra 2020-07-14T01:05:37 prefetch.2.10.7: 1) Downloading 'SRR11978433'... 2020-07-14T01:05:37 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:07:22 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:07:22 prefetch.2.10.7: 1) 'SRR11978433' was downloaded successfully 2020-07-14T01:07:22 prefetch.2.10.7: 'SRR11978433' has 0 unresolved dependencies Read 19345691 spots for SRR11978433/SRR11978433.sra Written 19345691 spots for SRR11978433/SRR11978433.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627369 ("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: 00:12:00 76140010 reads; of these: 76140010 (100.00%) were unpaired; of these: 67353929 (88.46%) aligned 0 times 6565435 (8.62%) aligned exactly 1 time 2220646 (2.92%) aligned >1 times 11.54% overall alignment rate Time searching: 00:12:00 Overall time: 00:12:00 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] 2400816 / 8786081 = 0.2733 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 10:23:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521285/SRX8521285.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521285/SRX8521285.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521285/SRX8521285.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521285/SRX8521285.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 10:23:53: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:23:53: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:24:00: 1000000 INFO @ Tue, 14 Jul 2020 10:24:08: 2000000 INFO @ Tue, 14 Jul 2020 10:24:15: 3000000 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 10:24:22: 4000000 INFO @ Tue, 14 Jul 2020 10:24:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521285/SRX8521285.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521285/SRX8521285.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521285/SRX8521285.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521285/SRX8521285.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 10:24:23: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:24:23: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:24:30: 5000000 INFO @ Tue, 14 Jul 2020 10:24:31: 1000000 INFO @ Tue, 14 Jul 2020 10:24:38: 2000000 INFO @ Tue, 14 Jul 2020 10:24:38: 6000000 INFO @ Tue, 14 Jul 2020 10:24:41: #1 tag size is determined as 66 bps INFO @ Tue, 14 Jul 2020 10:24:41: #1 tag size = 66 INFO @ Tue, 14 Jul 2020 10:24:41: #1 total tags in treatment: 6385265 INFO @ Tue, 14 Jul 2020 10:24:41: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:24:41: #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 10:24:41: #1 tags after filtering in treatment: 6385265 INFO @ Tue, 14 Jul 2020 10:24:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:24:41: #1 finished! INFO @ Tue, 14 Jul 2020 10:24:41: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:24:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:24:42: #2 number of paired peaks: 392 WARNING @ Tue, 14 Jul 2020 10:24:42: Fewer paired peaks (392) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 392 pairs to build model! INFO @ Tue, 14 Jul 2020 10:24:42: start model_add_line... INFO @ Tue, 14 Jul 2020 10:24:42: start X-correlation... INFO @ Tue, 14 Jul 2020 10:24:42: end of X-cor INFO @ Tue, 14 Jul 2020 10:24:42: #2 finished! INFO @ Tue, 14 Jul 2020 10:24:42: #2 predicted fragment length is 68 bps INFO @ Tue, 14 Jul 2020 10:24:42: #2 alternative fragment length(s) may be 68 bps INFO @ Tue, 14 Jul 2020 10:24:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521285/SRX8521285.05_model.r WARNING @ Tue, 14 Jul 2020 10:24:42: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:24:42: #2 You may need to consider one of the other alternative d(s): 68 WARNING @ Tue, 14 Jul 2020 10:24:42: #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 10:24:42: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:24:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:24:44: 3000000 INFO @ Tue, 14 Jul 2020 10:24:51: 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 10:24:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521285/SRX8521285.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521285/SRX8521285.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521285/SRX8521285.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521285/SRX8521285.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 10:24:53: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:24:53: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:24:54: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:24:58: 5000000 INFO @ Tue, 14 Jul 2020 10:25:01: 1000000 INFO @ Tue, 14 Jul 2020 10:25:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521285/SRX8521285.05_peaks.xls INFO @ Tue, 14 Jul 2020 10:25:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521285/SRX8521285.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:25:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521285/SRX8521285.05_summits.bed INFO @ Tue, 14 Jul 2020 10:25:01: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2191 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:25:05: 6000000 INFO @ Tue, 14 Jul 2020 10:25:08: #1 tag size is determined as 66 bps INFO @ Tue, 14 Jul 2020 10:25:08: #1 tag size = 66 INFO @ Tue, 14 Jul 2020 10:25:08: #1 total tags in treatment: 6385265 INFO @ Tue, 14 Jul 2020 10:25:08: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:25:08: #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 10:25:08: #1 tags after filtering in treatment: 6385265 INFO @ Tue, 14 Jul 2020 10:25:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:25:08: #1 finished! INFO @ Tue, 14 Jul 2020 10:25:08: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:25:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:25:08: 2000000 INFO @ Tue, 14 Jul 2020 10:25:08: #2 number of paired peaks: 392 WARNING @ Tue, 14 Jul 2020 10:25:08: Fewer paired peaks (392) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 392 pairs to build model! INFO @ Tue, 14 Jul 2020 10:25:08: start model_add_line... INFO @ Tue, 14 Jul 2020 10:25:08: start X-correlation... INFO @ Tue, 14 Jul 2020 10:25:08: end of X-cor INFO @ Tue, 14 Jul 2020 10:25:08: #2 finished! INFO @ Tue, 14 Jul 2020 10:25:08: #2 predicted fragment length is 68 bps INFO @ Tue, 14 Jul 2020 10:25:08: #2 alternative fragment length(s) may be 68 bps INFO @ Tue, 14 Jul 2020 10:25:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521285/SRX8521285.10_model.r WARNING @ Tue, 14 Jul 2020 10:25:08: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:25:08: #2 You may need to consider one of the other alternative d(s): 68 WARNING @ Tue, 14 Jul 2020 10:25:08: #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 10:25:08: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:25:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:25:14: 3000000 INFO @ Tue, 14 Jul 2020 10:25:20: 4000000 INFO @ Tue, 14 Jul 2020 10:25:21: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 10:25:27: 5000000 INFO @ Tue, 14 Jul 2020 10:25:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521285/SRX8521285.10_peaks.xls INFO @ Tue, 14 Jul 2020 10:25:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521285/SRX8521285.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:25:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521285/SRX8521285.10_summits.bed INFO @ Tue, 14 Jul 2020 10:25:28: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (874 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:25:33: 6000000 INFO @ Tue, 14 Jul 2020 10:25:36: #1 tag size is determined as 66 bps INFO @ Tue, 14 Jul 2020 10:25:36: #1 tag size = 66 INFO @ Tue, 14 Jul 2020 10:25:36: #1 total tags in treatment: 6385265 INFO @ Tue, 14 Jul 2020 10:25:36: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:25:36: #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 10:25:36: #1 tags after filtering in treatment: 6385265 INFO @ Tue, 14 Jul 2020 10:25:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:25:36: #1 finished! INFO @ Tue, 14 Jul 2020 10:25:36: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:25:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:25:36: #2 number of paired peaks: 392 WARNING @ Tue, 14 Jul 2020 10:25:36: Fewer paired peaks (392) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 392 pairs to build model! INFO @ Tue, 14 Jul 2020 10:25:36: start model_add_line... INFO @ Tue, 14 Jul 2020 10:25:36: start X-correlation... INFO @ Tue, 14 Jul 2020 10:25:36: end of X-cor INFO @ Tue, 14 Jul 2020 10:25:36: #2 finished! INFO @ Tue, 14 Jul 2020 10:25:36: #2 predicted fragment length is 68 bps INFO @ Tue, 14 Jul 2020 10:25:36: #2 alternative fragment length(s) may be 68 bps INFO @ Tue, 14 Jul 2020 10:25:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521285/SRX8521285.20_model.r WARNING @ Tue, 14 Jul 2020 10:25:36: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:25:36: #2 You may need to consider one of the other alternative d(s): 68 WARNING @ Tue, 14 Jul 2020 10:25:36: #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 10:25:36: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:25:36: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 10:25:50: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:25:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521285/SRX8521285.20_peaks.xls INFO @ Tue, 14 Jul 2020 10:25:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521285/SRX8521285.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:25:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521285/SRX8521285.20_summits.bed INFO @ Tue, 14 Jul 2020 10:25:57: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (237 records, 4 fields): 2 millis CompletedMACS2peakCalling