Job ID = 6627257 SRX = SRX8521329 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-14T01:38:34 prefetch.2.10.7: 1) Downloading 'SRR11977985'... 2020-07-14T01:38:34 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:39:41 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:39:41 prefetch.2.10.7: 'SRR11977985' is valid 2020-07-14T01:39:41 prefetch.2.10.7: 1) 'SRR11977985' was downloaded successfully 2020-07-14T01:39:41 prefetch.2.10.7: 'SRR11977985' has 0 unresolved dependencies Read 10900066 spots for SRR11977985/SRR11977985.sra Written 10900066 spots for SRR11977985/SRR11977985.sra 2020-07-14T01:40:27 prefetch.2.10.7: 1) Downloading 'SRR11977986'... 2020-07-14T01:40:27 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:41:31 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:41:32 prefetch.2.10.7: 'SRR11977986' is valid 2020-07-14T01:41:32 prefetch.2.10.7: 1) 'SRR11977986' was downloaded successfully 2020-07-14T01:41:32 prefetch.2.10.7: 'SRR11977986' has 0 unresolved dependencies Read 10730846 spots for SRR11977986/SRR11977986.sra Written 10730846 spots for SRR11977986/SRR11977986.sra 2020-07-14T01:42:17 prefetch.2.10.7: 1) Downloading 'SRR11977987'... 2020-07-14T01:42:17 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:43:32 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:43:32 prefetch.2.10.7: 'SRR11977987' is valid 2020-07-14T01:43:32 prefetch.2.10.7: 1) 'SRR11977987' was downloaded successfully 2020-07-14T01:43:32 prefetch.2.10.7: 'SRR11977987' has 0 unresolved dependencies Read 10842167 spots for SRR11977987/SRR11977987.sra Written 10842167 spots for SRR11977987/SRR11977987.sra 2020-07-14T01:44:17 prefetch.2.10.7: 1) Downloading 'SRR11977988'... 2020-07-14T01:44:17 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:45:26 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:45:26 prefetch.2.10.7: 'SRR11977988' is valid 2020-07-14T01:45:26 prefetch.2.10.7: 1) 'SRR11977988' was downloaded successfully 2020-07-14T01:45:26 prefetch.2.10.7: 'SRR11977988' has 0 unresolved dependencies Read 11166075 spots for SRR11977988/SRR11977988.sra Written 11166075 spots for SRR11977988/SRR11977988.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627459 ("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: 00:07:03 43639154 reads; of these: 43639154 (100.00%) were unpaired; of these: 36860252 (84.47%) aligned 0 times 5274701 (12.09%) aligned exactly 1 time 1504201 (3.45%) aligned >1 times 15.53% overall alignment rate Time searching: 00:07:03 Overall time: 00:07:03 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] 1170809 / 6778902 = 0.1727 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 10:55:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521329/SRX8521329.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521329/SRX8521329.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521329/SRX8521329.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521329/SRX8521329.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 10:55:36: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:55:36: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:55:42: 1000000 INFO @ Tue, 14 Jul 2020 10:55:47: 2000000 INFO @ Tue, 14 Jul 2020 10:55:53: 3000000 INFO @ Tue, 14 Jul 2020 10:55:59: 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 10:56:05: 5000000 INFO @ Tue, 14 Jul 2020 10:56:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521329/SRX8521329.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521329/SRX8521329.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521329/SRX8521329.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521329/SRX8521329.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 10:56:05: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:56:05: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:56:08: #1 tag size is determined as 58 bps INFO @ Tue, 14 Jul 2020 10:56:08: #1 tag size = 58 INFO @ Tue, 14 Jul 2020 10:56:08: #1 total tags in treatment: 5608093 INFO @ Tue, 14 Jul 2020 10:56:08: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:56:09: #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 10:56:09: #1 tags after filtering in treatment: 5608093 INFO @ Tue, 14 Jul 2020 10:56:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:56:09: #1 finished! INFO @ Tue, 14 Jul 2020 10:56:09: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:56:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:56:09: #2 number of paired peaks: 419 WARNING @ Tue, 14 Jul 2020 10:56:09: Fewer paired peaks (419) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 419 pairs to build model! INFO @ Tue, 14 Jul 2020 10:56:09: start model_add_line... INFO @ Tue, 14 Jul 2020 10:56:09: start X-correlation... INFO @ Tue, 14 Jul 2020 10:56:09: end of X-cor INFO @ Tue, 14 Jul 2020 10:56:09: #2 finished! INFO @ Tue, 14 Jul 2020 10:56:09: #2 predicted fragment length is 50 bps INFO @ Tue, 14 Jul 2020 10:56:09: #2 alternative fragment length(s) may be 50,546 bps INFO @ Tue, 14 Jul 2020 10:56:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521329/SRX8521329.05_model.r WARNING @ Tue, 14 Jul 2020 10:56:09: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:56:09: #2 You may need to consider one of the other alternative d(s): 50,546 WARNING @ Tue, 14 Jul 2020 10:56:09: #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 10:56:09: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:56:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:56:11: 1000000 INFO @ Tue, 14 Jul 2020 10:56:17: 2000000 INFO @ Tue, 14 Jul 2020 10:56:22: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:56:22: 3000000 INFO @ Tue, 14 Jul 2020 10:56:28: 4000000 INFO @ Tue, 14 Jul 2020 10:56:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521329/SRX8521329.05_peaks.xls INFO @ Tue, 14 Jul 2020 10:56:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521329/SRX8521329.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:56:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521329/SRX8521329.05_summits.bed INFO @ Tue, 14 Jul 2020 10:56:28: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1765 records, 4 fields): 3 millis CompletedMACS2peakCalling 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 10:56:34: 5000000 INFO @ Tue, 14 Jul 2020 10:56:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521329/SRX8521329.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521329/SRX8521329.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521329/SRX8521329.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521329/SRX8521329.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 10:56:35: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:56:35: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:56:37: #1 tag size is determined as 58 bps INFO @ Tue, 14 Jul 2020 10:56:37: #1 tag size = 58 INFO @ Tue, 14 Jul 2020 10:56:37: #1 total tags in treatment: 5608093 INFO @ Tue, 14 Jul 2020 10:56:37: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:56:37: #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 10:56:37: #1 tags after filtering in treatment: 5608093 INFO @ Tue, 14 Jul 2020 10:56:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:56:37: #1 finished! INFO @ Tue, 14 Jul 2020 10:56:37: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:56:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:56:38: #2 number of paired peaks: 419 WARNING @ Tue, 14 Jul 2020 10:56:38: Fewer paired peaks (419) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 419 pairs to build model! INFO @ Tue, 14 Jul 2020 10:56:38: start model_add_line... INFO @ Tue, 14 Jul 2020 10:56:38: start X-correlation... INFO @ Tue, 14 Jul 2020 10:56:38: end of X-cor INFO @ Tue, 14 Jul 2020 10:56:38: #2 finished! INFO @ Tue, 14 Jul 2020 10:56:38: #2 predicted fragment length is 50 bps INFO @ Tue, 14 Jul 2020 10:56:38: #2 alternative fragment length(s) may be 50,546 bps INFO @ Tue, 14 Jul 2020 10:56:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521329/SRX8521329.10_model.r WARNING @ Tue, 14 Jul 2020 10:56:38: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:56:38: #2 You may need to consider one of the other alternative d(s): 50,546 WARNING @ Tue, 14 Jul 2020 10:56:38: #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 10:56:38: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:56:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:56:41: 1000000 INFO @ Tue, 14 Jul 2020 10:56:47: 2000000 INFO @ Tue, 14 Jul 2020 10:56:50: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:56:53: 3000000 INFO @ Tue, 14 Jul 2020 10:56:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521329/SRX8521329.10_peaks.xls INFO @ Tue, 14 Jul 2020 10:56:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521329/SRX8521329.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:56:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521329/SRX8521329.10_summits.bed INFO @ Tue, 14 Jul 2020 10:56:57: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (765 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:56:59: 4000000 INFO @ Tue, 14 Jul 2020 10:57:04: 5000000 INFO @ Tue, 14 Jul 2020 10:57:08: #1 tag size is determined as 58 bps INFO @ Tue, 14 Jul 2020 10:57:08: #1 tag size = 58 INFO @ Tue, 14 Jul 2020 10:57:08: #1 total tags in treatment: 5608093 INFO @ Tue, 14 Jul 2020 10:57:08: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:57:08: #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 10:57:08: #1 tags after filtering in treatment: 5608093 INFO @ Tue, 14 Jul 2020 10:57:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:57:08: #1 finished! INFO @ Tue, 14 Jul 2020 10:57:08: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:57:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:57:08: #2 number of paired peaks: 419 WARNING @ Tue, 14 Jul 2020 10:57:08: Fewer paired peaks (419) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 419 pairs to build model! INFO @ Tue, 14 Jul 2020 10:57:08: start model_add_line... INFO @ Tue, 14 Jul 2020 10:57:08: start X-correlation... INFO @ Tue, 14 Jul 2020 10:57:09: end of X-cor INFO @ Tue, 14 Jul 2020 10:57:09: #2 finished! INFO @ Tue, 14 Jul 2020 10:57:09: #2 predicted fragment length is 50 bps INFO @ Tue, 14 Jul 2020 10:57:09: #2 alternative fragment length(s) may be 50,546 bps INFO @ Tue, 14 Jul 2020 10:57:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521329/SRX8521329.20_model.r WARNING @ Tue, 14 Jul 2020 10:57:09: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:57:09: #2 You may need to consider one of the other alternative d(s): 50,546 WARNING @ Tue, 14 Jul 2020 10:57:09: #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 10:57:09: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:57:09: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 10:57:21: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 10:57:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521329/SRX8521329.20_peaks.xls INFO @ Tue, 14 Jul 2020 10:57:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521329/SRX8521329.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:57:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521329/SRX8521329.20_summits.bed INFO @ Tue, 14 Jul 2020 10:57:27: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (150 records, 4 fields): 1 millis CompletedMACS2peakCalling