Job ID = 6627270 SRX = SRX8521338 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-14T01:45:26 prefetch.2.10.7: 1) Downloading 'SRR11978560'... 2020-07-14T01:45:26 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:47:34 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:47:35 prefetch.2.10.7: 'SRR11978560' is valid 2020-07-14T01:47:35 prefetch.2.10.7: 1) 'SRR11978560' was downloaded successfully 2020-07-14T01:47:35 prefetch.2.10.7: 'SRR11978560' has 0 unresolved dependencies Read 16642645 spots for SRR11978560/SRR11978560.sra Written 16642645 spots for SRR11978560/SRR11978560.sra 2020-07-14T01:48:42 prefetch.2.10.7: 1) Downloading 'SRR11978561'... 2020-07-14T01:48:42 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:50:38 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:50:39 prefetch.2.10.7: 'SRR11978561' is valid 2020-07-14T01:50:39 prefetch.2.10.7: 1) 'SRR11978561' was downloaded successfully 2020-07-14T01:50:39 prefetch.2.10.7: 'SRR11978561' has 0 unresolved dependencies Read 16256531 spots for SRR11978561/SRR11978561.sra Written 16256531 spots for SRR11978561/SRR11978561.sra 2020-07-14T01:51:48 prefetch.2.10.7: 1) Downloading 'SRR11978562'... 2020-07-14T01:51:48 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:55:18 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:55:19 prefetch.2.10.7: 'SRR11978562' is valid 2020-07-14T01:55:19 prefetch.2.10.7: 1) 'SRR11978562' was downloaded successfully 2020-07-14T01:55:19 prefetch.2.10.7: 'SRR11978562' has 0 unresolved dependencies Read 16890989 spots for SRR11978562/SRR11978562.sra Written 16890989 spots for SRR11978562/SRR11978562.sra 2020-07-14T01:56:30 prefetch.2.10.7: 1) Downloading 'SRR11978563'... 2020-07-14T01:56:30 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:58:35 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:58:36 prefetch.2.10.7: 'SRR11978563' is valid 2020-07-14T01:58:36 prefetch.2.10.7: 1) 'SRR11978563' was downloaded successfully 2020-07-14T01:58:36 prefetch.2.10.7: 'SRR11978563' has 0 unresolved dependencies Read 16650466 spots for SRR11978563/SRR11978563.sra Written 16650466 spots for SRR11978563/SRR11978563.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627540 ("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: 00:14:08 66440631 reads; of these: 66440631 (100.00%) were unpaired; of these: 52934026 (79.67%) aligned 0 times 9470423 (14.25%) aligned exactly 1 time 4036182 (6.07%) aligned >1 times 20.33% overall alignment rate Time searching: 00:14:08 Overall time: 00:14:08 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] 2952548 / 13506605 = 0.2186 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 11:18:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521338/SRX8521338.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521338/SRX8521338.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521338/SRX8521338.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521338/SRX8521338.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 11:18:24: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:18:24: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:18:31: 1000000 INFO @ Tue, 14 Jul 2020 11:18:38: 2000000 INFO @ Tue, 14 Jul 2020 11:18:45: 3000000 INFO @ Tue, 14 Jul 2020 11:18:52: 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 11:18:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521338/SRX8521338.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521338/SRX8521338.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521338/SRX8521338.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521338/SRX8521338.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 11:18:54: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:18:54: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:18:59: 5000000 INFO @ Tue, 14 Jul 2020 11:19:02: 1000000 INFO @ Tue, 14 Jul 2020 11:19:06: 6000000 INFO @ Tue, 14 Jul 2020 11:19:09: 2000000 INFO @ Tue, 14 Jul 2020 11:19:14: 7000000 INFO @ Tue, 14 Jul 2020 11:19:17: 3000000 INFO @ Tue, 14 Jul 2020 11:19:21: 8000000 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 11:19:24: 4000000 INFO @ Tue, 14 Jul 2020 11:19:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521338/SRX8521338.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521338/SRX8521338.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521338/SRX8521338.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521338/SRX8521338.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 11:19:24: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:19:24: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:19:28: 9000000 INFO @ Tue, 14 Jul 2020 11:19:31: 5000000 INFO @ Tue, 14 Jul 2020 11:19:32: 1000000 INFO @ Tue, 14 Jul 2020 11:19:36: 10000000 INFO @ Tue, 14 Jul 2020 11:19:39: 6000000 INFO @ Tue, 14 Jul 2020 11:19:40: 2000000 INFO @ Tue, 14 Jul 2020 11:19:40: #1 tag size is determined as 54 bps INFO @ Tue, 14 Jul 2020 11:19:40: #1 tag size = 54 INFO @ Tue, 14 Jul 2020 11:19:40: #1 total tags in treatment: 10554057 INFO @ Tue, 14 Jul 2020 11:19:40: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:19:40: #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 11:19:40: #1 tags after filtering in treatment: 10554057 INFO @ Tue, 14 Jul 2020 11:19:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:19:40: #1 finished! INFO @ Tue, 14 Jul 2020 11:19:40: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:19:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:19:41: #2 number of paired peaks: 122 WARNING @ Tue, 14 Jul 2020 11:19:41: Fewer paired peaks (122) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 122 pairs to build model! INFO @ Tue, 14 Jul 2020 11:19:41: start model_add_line... INFO @ Tue, 14 Jul 2020 11:19:41: start X-correlation... INFO @ Tue, 14 Jul 2020 11:19:41: end of X-cor INFO @ Tue, 14 Jul 2020 11:19:41: #2 finished! INFO @ Tue, 14 Jul 2020 11:19:41: #2 predicted fragment length is 53 bps INFO @ Tue, 14 Jul 2020 11:19:41: #2 alternative fragment length(s) may be 53 bps INFO @ Tue, 14 Jul 2020 11:19:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521338/SRX8521338.05_model.r WARNING @ Tue, 14 Jul 2020 11:19:41: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:19:41: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Tue, 14 Jul 2020 11:19:41: #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 11:19:41: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:19:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:19:46: 7000000 INFO @ Tue, 14 Jul 2020 11:19:47: 3000000 INFO @ Tue, 14 Jul 2020 11:19:53: 8000000 INFO @ Tue, 14 Jul 2020 11:19:54: 4000000 INFO @ Tue, 14 Jul 2020 11:20:00: 9000000 INFO @ Tue, 14 Jul 2020 11:20:01: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:20:02: 5000000 INFO @ Tue, 14 Jul 2020 11:20:07: 10000000 INFO @ Tue, 14 Jul 2020 11:20:09: 6000000 INFO @ Tue, 14 Jul 2020 11:20:11: #1 tag size is determined as 54 bps INFO @ Tue, 14 Jul 2020 11:20:11: #1 tag size = 54 INFO @ Tue, 14 Jul 2020 11:20:11: #1 total tags in treatment: 10554057 INFO @ Tue, 14 Jul 2020 11:20:11: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:20:11: #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 11:20:11: #1 tags after filtering in treatment: 10554057 INFO @ Tue, 14 Jul 2020 11:20:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:20:11: #1 finished! INFO @ Tue, 14 Jul 2020 11:20:11: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:20:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:20:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521338/SRX8521338.05_peaks.xls INFO @ Tue, 14 Jul 2020 11:20:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521338/SRX8521338.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:20:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521338/SRX8521338.05_summits.bed INFO @ Tue, 14 Jul 2020 11:20:12: Done! INFO @ Tue, 14 Jul 2020 11:20:12: #2 number of paired peaks: 122 WARNING @ Tue, 14 Jul 2020 11:20:12: Fewer paired peaks (122) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 122 pairs to build model! INFO @ Tue, 14 Jul 2020 11:20:12: start model_add_line... pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1818 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 11:20:12: start X-correlation... INFO @ Tue, 14 Jul 2020 11:20:12: end of X-cor INFO @ Tue, 14 Jul 2020 11:20:12: #2 finished! INFO @ Tue, 14 Jul 2020 11:20:12: #2 predicted fragment length is 53 bps INFO @ Tue, 14 Jul 2020 11:20:12: #2 alternative fragment length(s) may be 53 bps INFO @ Tue, 14 Jul 2020 11:20:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521338/SRX8521338.10_model.r WARNING @ Tue, 14 Jul 2020 11:20:12: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:20:12: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Tue, 14 Jul 2020 11:20:12: #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 11:20:12: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:20:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:20:16: 7000000 INFO @ Tue, 14 Jul 2020 11:20:23: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 11:20:30: 9000000 INFO @ Tue, 14 Jul 2020 11:20:33: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:20:38: 10000000 INFO @ Tue, 14 Jul 2020 11:20:41: #1 tag size is determined as 54 bps INFO @ Tue, 14 Jul 2020 11:20:41: #1 tag size = 54 INFO @ Tue, 14 Jul 2020 11:20:41: #1 total tags in treatment: 10554057 INFO @ Tue, 14 Jul 2020 11:20:41: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:20:41: #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 11:20:42: #1 tags after filtering in treatment: 10554057 INFO @ Tue, 14 Jul 2020 11:20:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:20:42: #1 finished! INFO @ Tue, 14 Jul 2020 11:20:42: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:20:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:20:42: #2 number of paired peaks: 122 WARNING @ Tue, 14 Jul 2020 11:20:42: Fewer paired peaks (122) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 122 pairs to build model! INFO @ Tue, 14 Jul 2020 11:20:42: start model_add_line... INFO @ Tue, 14 Jul 2020 11:20:42: start X-correlation... INFO @ Tue, 14 Jul 2020 11:20:42: end of X-cor INFO @ Tue, 14 Jul 2020 11:20:42: #2 finished! INFO @ Tue, 14 Jul 2020 11:20:42: #2 predicted fragment length is 53 bps INFO @ Tue, 14 Jul 2020 11:20:42: #2 alternative fragment length(s) may be 53 bps INFO @ Tue, 14 Jul 2020 11:20:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521338/SRX8521338.20_model.r WARNING @ Tue, 14 Jul 2020 11:20:42: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:20:42: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Tue, 14 Jul 2020 11:20:42: #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 11:20:42: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:20:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:20:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521338/SRX8521338.10_peaks.xls INFO @ Tue, 14 Jul 2020 11:20:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521338/SRX8521338.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:20:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521338/SRX8521338.10_summits.bed INFO @ Tue, 14 Jul 2020 11:20:43: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (1101 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 11:21:03: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:21:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521338/SRX8521338.20_peaks.xls INFO @ Tue, 14 Jul 2020 11:21:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521338/SRX8521338.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:21:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521338/SRX8521338.20_summits.bed INFO @ Tue, 14 Jul 2020 11:21:14: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (478 records, 4 fields): 2 millis CompletedMACS2peakCalling