Job ID = 6627296 SRX = SRX8521358 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-14T01:53:44 prefetch.2.10.7: 1) Downloading 'SRR11978086'... 2020-07-14T01:53:44 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:56:03 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:56:04 prefetch.2.10.7: 'SRR11978086' is valid 2020-07-14T01:56:04 prefetch.2.10.7: 1) 'SRR11978086' was downloaded successfully 2020-07-14T01:56:04 prefetch.2.10.7: 'SRR11978086' has 0 unresolved dependencies Read 15502793 spots for SRR11978086/SRR11978086.sra Written 15502793 spots for SRR11978086/SRR11978086.sra 2020-07-14T01:57:11 prefetch.2.10.7: 1) Downloading 'SRR11978087'... 2020-07-14T01:57:11 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:58:56 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:58:57 prefetch.2.10.7: 'SRR11978087' is valid 2020-07-14T01:58:57 prefetch.2.10.7: 1) 'SRR11978087' was downloaded successfully 2020-07-14T01:58:57 prefetch.2.10.7: 'SRR11978087' has 0 unresolved dependencies Read 15058231 spots for SRR11978087/SRR11978087.sra Written 15058231 spots for SRR11978087/SRR11978087.sra 2020-07-14T02:00:00 prefetch.2.10.7: 1) Downloading 'SRR11978088'... 2020-07-14T02:00:00 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:02:12 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:02:13 prefetch.2.10.7: 'SRR11978088' is valid 2020-07-14T02:02:13 prefetch.2.10.7: 1) 'SRR11978088' was downloaded successfully 2020-07-14T02:02:13 prefetch.2.10.7: 'SRR11978088' has 0 unresolved dependencies Read 15646500 spots for SRR11978088/SRR11978088.sra Written 15646500 spots for SRR11978088/SRR11978088.sra 2020-07-14T02:03:19 prefetch.2.10.7: 1) Downloading 'SRR11978089'... 2020-07-14T02:03:19 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T02:04:37 prefetch.2.10.7: HTTPS download succeed 2020-07-14T02:04:38 prefetch.2.10.7: 'SRR11978089' is valid 2020-07-14T02:04:38 prefetch.2.10.7: 1) 'SRR11978089' was downloaded successfully 2020-07-14T02:04:38 prefetch.2.10.7: 'SRR11978089' has 0 unresolved dependencies Read 15557200 spots for SRR11978089/SRR11978089.sra Written 15557200 spots for SRR11978089/SRR11978089.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627546 ("srTdm6") has been submitted Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:09:36 61764724 reads; of these: 61764724 (100.00%) were unpaired; of these: 54417155 (88.10%) aligned 0 times 5363003 (8.68%) aligned exactly 1 time 1984566 (3.21%) aligned >1 times 11.90% overall alignment rate Time searching: 00:09:37 Overall time: 00:09:37 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] 1545364 / 7347569 = 0.2103 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 11:18:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521358/SRX8521358.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521358/SRX8521358.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521358/SRX8521358.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521358/SRX8521358.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 11:18:10: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:18:10: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:18:15: 1000000 INFO @ Tue, 14 Jul 2020 11:18:20: 2000000 INFO @ Tue, 14 Jul 2020 11:18:26: 3000000 INFO @ Tue, 14 Jul 2020 11:18:31: 4000000 INFO @ Tue, 14 Jul 2020 11:18:36: 5000000 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 11:18:40: #1 tag size is determined as 67 bps INFO @ Tue, 14 Jul 2020 11:18:40: #1 tag size = 67 INFO @ Tue, 14 Jul 2020 11:18:40: #1 total tags in treatment: 5802205 INFO @ Tue, 14 Jul 2020 11:18:40: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:18:40: #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 11:18:40: #1 tags after filtering in treatment: 5802205 INFO @ Tue, 14 Jul 2020 11:18:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:18:40: #1 finished! INFO @ Tue, 14 Jul 2020 11:18:40: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:18:40: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:18:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521358/SRX8521358.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521358/SRX8521358.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521358/SRX8521358.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521358/SRX8521358.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 11:18:40: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:18:40: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:18:40: #2 number of paired peaks: 478 WARNING @ Tue, 14 Jul 2020 11:18:40: Fewer paired peaks (478) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 478 pairs to build model! INFO @ Tue, 14 Jul 2020 11:18:40: start model_add_line... INFO @ Tue, 14 Jul 2020 11:18:40: start X-correlation... INFO @ Tue, 14 Jul 2020 11:18:40: end of X-cor INFO @ Tue, 14 Jul 2020 11:18:40: #2 finished! INFO @ Tue, 14 Jul 2020 11:18:40: #2 predicted fragment length is 68 bps INFO @ Tue, 14 Jul 2020 11:18:40: #2 alternative fragment length(s) may be 68 bps INFO @ Tue, 14 Jul 2020 11:18:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521358/SRX8521358.05_model.r WARNING @ Tue, 14 Jul 2020 11:18:40: #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 11:18:40: #2 You may need to consider one of the other alternative d(s): 68 WARNING @ Tue, 14 Jul 2020 11:18:40: #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 11:18:40: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:18:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:18:45: 1000000 INFO @ Tue, 14 Jul 2020 11:18:50: 2000000 INFO @ Tue, 14 Jul 2020 11:18:53: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:18:55: 3000000 INFO @ Tue, 14 Jul 2020 11:18:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521358/SRX8521358.05_peaks.xls INFO @ Tue, 14 Jul 2020 11:18:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521358/SRX8521358.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:18:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521358/SRX8521358.05_summits.bed INFO @ Tue, 14 Jul 2020 11:18:59: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2604 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 11:19:01: 4000000 INFO @ Tue, 14 Jul 2020 11:19:06: 5000000 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 11:19:10: #1 tag size is determined as 67 bps INFO @ Tue, 14 Jul 2020 11:19:10: #1 tag size = 67 INFO @ Tue, 14 Jul 2020 11:19:10: #1 total tags in treatment: 5802205 INFO @ Tue, 14 Jul 2020 11:19:10: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:19:10: #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 11:19:10: #1 tags after filtering in treatment: 5802205 INFO @ Tue, 14 Jul 2020 11:19:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:19:10: #1 finished! INFO @ Tue, 14 Jul 2020 11:19:10: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:19:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:19:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521358/SRX8521358.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521358/SRX8521358.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521358/SRX8521358.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521358/SRX8521358.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 11:19:10: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:19:10: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:19:10: #2 number of paired peaks: 478 WARNING @ Tue, 14 Jul 2020 11:19:10: Fewer paired peaks (478) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 478 pairs to build model! INFO @ Tue, 14 Jul 2020 11:19:10: start model_add_line... INFO @ Tue, 14 Jul 2020 11:19:10: start X-correlation... INFO @ Tue, 14 Jul 2020 11:19:10: end of X-cor INFO @ Tue, 14 Jul 2020 11:19:10: #2 finished! INFO @ Tue, 14 Jul 2020 11:19:10: #2 predicted fragment length is 68 bps INFO @ Tue, 14 Jul 2020 11:19:10: #2 alternative fragment length(s) may be 68 bps INFO @ Tue, 14 Jul 2020 11:19:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521358/SRX8521358.10_model.r WARNING @ Tue, 14 Jul 2020 11:19:10: #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 11:19:10: #2 You may need to consider one of the other alternative d(s): 68 WARNING @ Tue, 14 Jul 2020 11:19:10: #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 11:19:10: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:19:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:19:15: 1000000 INFO @ Tue, 14 Jul 2020 11:19:20: 2000000 INFO @ Tue, 14 Jul 2020 11:19:23: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:19:25: 3000000 INFO @ Tue, 14 Jul 2020 11:19:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521358/SRX8521358.10_peaks.xls INFO @ Tue, 14 Jul 2020 11:19:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521358/SRX8521358.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:19:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521358/SRX8521358.10_summits.bed INFO @ Tue, 14 Jul 2020 11:19:29: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1073 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 11:19:31: 4000000 INFO @ Tue, 14 Jul 2020 11:19:36: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 11:19:40: #1 tag size is determined as 67 bps INFO @ Tue, 14 Jul 2020 11:19:40: #1 tag size = 67 INFO @ Tue, 14 Jul 2020 11:19:40: #1 total tags in treatment: 5802205 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: 5802205 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 11:19:40: #2 number of paired peaks: 478 WARNING @ Tue, 14 Jul 2020 11:19:40: Fewer paired peaks (478) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 478 pairs to build model! INFO @ Tue, 14 Jul 2020 11:19:40: start model_add_line... INFO @ Tue, 14 Jul 2020 11:19:40: start X-correlation... INFO @ Tue, 14 Jul 2020 11:19:40: end of X-cor INFO @ Tue, 14 Jul 2020 11:19:40: #2 finished! INFO @ Tue, 14 Jul 2020 11:19:40: #2 predicted fragment length is 68 bps INFO @ Tue, 14 Jul 2020 11:19:40: #2 alternative fragment length(s) may be 68 bps INFO @ Tue, 14 Jul 2020 11:19:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521358/SRX8521358.20_model.r WARNING @ Tue, 14 Jul 2020 11:19:40: #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 11:19:40: #2 You may need to consider one of the other alternative d(s): 68 WARNING @ Tue, 14 Jul 2020 11:19:40: #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 11:19:40: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:19:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:19:53: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 11:19:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521358/SRX8521358.20_peaks.xls INFO @ Tue, 14 Jul 2020 11:19:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521358/SRX8521358.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:19:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521358/SRX8521358.20_summits.bed INFO @ Tue, 14 Jul 2020 11:19:59: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (303 records, 4 fields): 2 millis CompletedMACS2peakCalling