Job ID = 6627244 SRX = SRX8521320 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-14T01:35:01 prefetch.2.10.7: 1) Downloading 'SRR11977937'... 2020-07-14T01:35:01 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:36:31 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:36:32 prefetch.2.10.7: 'SRR11977937' is valid 2020-07-14T01:36:32 prefetch.2.10.7: 1) 'SRR11977937' was downloaded successfully 2020-07-14T01:36:32 prefetch.2.10.7: 'SRR11977937' has 0 unresolved dependencies Read 11396765 spots for SRR11977937/SRR11977937.sra Written 11396765 spots for SRR11977937/SRR11977937.sra 2020-07-14T01:37:23 prefetch.2.10.7: 1) Downloading 'SRR11977938'... 2020-07-14T01:37:23 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:38:21 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:38:21 prefetch.2.10.7: 'SRR11977938' is valid 2020-07-14T01:38:21 prefetch.2.10.7: 1) 'SRR11977938' was downloaded successfully 2020-07-14T01:38:21 prefetch.2.10.7: 'SRR11977938' has 0 unresolved dependencies Read 10994450 spots for SRR11977938/SRR11977938.sra Written 10994450 spots for SRR11977938/SRR11977938.sra 2020-07-14T01:39:11 prefetch.2.10.7: 1) Downloading 'SRR11977939'... 2020-07-14T01:39:11 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:40:22 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:40:22 prefetch.2.10.7: 'SRR11977939' is valid 2020-07-14T01:40:22 prefetch.2.10.7: 1) 'SRR11977939' was downloaded successfully 2020-07-14T01:40:22 prefetch.2.10.7: 'SRR11977939' has 0 unresolved dependencies Read 11342411 spots for SRR11977939/SRR11977939.sra Written 11342411 spots for SRR11977939/SRR11977939.sra 2020-07-14T01:41:10 prefetch.2.10.7: 1) Downloading 'SRR11977940'... 2020-07-14T01:41:10 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:42:48 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:42:48 prefetch.2.10.7: 'SRR11977940' is valid 2020-07-14T01:42:48 prefetch.2.10.7: 1) 'SRR11977940' was downloaded successfully 2020-07-14T01:42:48 prefetch.2.10.7: 'SRR11977940' has 0 unresolved dependencies Read 11055160 spots for SRR11977940/SRR11977940.sra Written 11055160 spots for SRR11977940/SRR11977940.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627452 ("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: 00:06:43 44788786 reads; of these: 44788786 (100.00%) were unpaired; of these: 36254855 (80.95%) aligned 0 times 6669179 (14.89%) aligned exactly 1 time 1864752 (4.16%) aligned >1 times 19.05% overall alignment rate Time searching: 00:06:43 Overall time: 00:06:43 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] 1643076 / 8533931 = 0.1925 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 10:53:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521320/SRX8521320.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521320/SRX8521320.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521320/SRX8521320.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521320/SRX8521320.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 10:53:17: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:53:17: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:53:23: 1000000 INFO @ Tue, 14 Jul 2020 10:53:28: 2000000 INFO @ Tue, 14 Jul 2020 10:53:34: 3000000 INFO @ Tue, 14 Jul 2020 10:53:40: 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 10:53:46: 5000000 INFO @ Tue, 14 Jul 2020 10:53:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521320/SRX8521320.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521320/SRX8521320.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521320/SRX8521320.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521320/SRX8521320.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 10:53:47: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:53:47: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:53:53: 6000000 INFO @ Tue, 14 Jul 2020 10:53:54: 1000000 INFO @ Tue, 14 Jul 2020 10:53:59: #1 tag size is determined as 59 bps INFO @ Tue, 14 Jul 2020 10:53:59: #1 tag size = 59 INFO @ Tue, 14 Jul 2020 10:53:59: #1 total tags in treatment: 6890855 INFO @ Tue, 14 Jul 2020 10:53:59: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:53:59: #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 10:53:59: #1 tags after filtering in treatment: 6890855 INFO @ Tue, 14 Jul 2020 10:53:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:53:59: #1 finished! INFO @ Tue, 14 Jul 2020 10:53:59: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:53:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:54:00: #2 number of paired peaks: 304 WARNING @ Tue, 14 Jul 2020 10:54:00: Fewer paired peaks (304) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 304 pairs to build model! INFO @ Tue, 14 Jul 2020 10:54:00: start model_add_line... INFO @ Tue, 14 Jul 2020 10:54:00: start X-correlation... INFO @ Tue, 14 Jul 2020 10:54:00: end of X-cor INFO @ Tue, 14 Jul 2020 10:54:00: #2 finished! INFO @ Tue, 14 Jul 2020 10:54:00: #2 predicted fragment length is 49 bps INFO @ Tue, 14 Jul 2020 10:54:00: #2 alternative fragment length(s) may be 4,49,550 bps INFO @ Tue, 14 Jul 2020 10:54:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521320/SRX8521320.05_model.r WARNING @ Tue, 14 Jul 2020 10:54:00: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:54:00: #2 You may need to consider one of the other alternative d(s): 4,49,550 WARNING @ Tue, 14 Jul 2020 10:54:00: #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 10:54:00: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:54:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:54:01: 2000000 INFO @ Tue, 14 Jul 2020 10:54:07: 3000000 INFO @ Tue, 14 Jul 2020 10:54:14: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:54:14: 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 10:54:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521320/SRX8521320.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521320/SRX8521320.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521320/SRX8521320.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521320/SRX8521320.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 10:54:17: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:54:17: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:54:21: 5000000 INFO @ Tue, 14 Jul 2020 10:54:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521320/SRX8521320.05_peaks.xls INFO @ Tue, 14 Jul 2020 10:54:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521320/SRX8521320.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:54:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521320/SRX8521320.05_summits.bed INFO @ Tue, 14 Jul 2020 10:54:21: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1703 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:54:24: 1000000 INFO @ Tue, 14 Jul 2020 10:54:28: 6000000 INFO @ Tue, 14 Jul 2020 10:54:31: 2000000 INFO @ Tue, 14 Jul 2020 10:54:34: #1 tag size is determined as 59 bps INFO @ Tue, 14 Jul 2020 10:54:34: #1 tag size = 59 INFO @ Tue, 14 Jul 2020 10:54:34: #1 total tags in treatment: 6890855 INFO @ Tue, 14 Jul 2020 10:54:34: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:54:34: #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 10:54:34: #1 tags after filtering in treatment: 6890855 INFO @ Tue, 14 Jul 2020 10:54:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:54:34: #1 finished! INFO @ Tue, 14 Jul 2020 10:54:34: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:54:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:54:35: #2 number of paired peaks: 304 WARNING @ Tue, 14 Jul 2020 10:54:35: Fewer paired peaks (304) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 304 pairs to build model! INFO @ Tue, 14 Jul 2020 10:54:35: start model_add_line... INFO @ Tue, 14 Jul 2020 10:54:35: start X-correlation... INFO @ Tue, 14 Jul 2020 10:54:35: end of X-cor INFO @ Tue, 14 Jul 2020 10:54:35: #2 finished! INFO @ Tue, 14 Jul 2020 10:54:35: #2 predicted fragment length is 49 bps INFO @ Tue, 14 Jul 2020 10:54:35: #2 alternative fragment length(s) may be 4,49,550 bps INFO @ Tue, 14 Jul 2020 10:54:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521320/SRX8521320.10_model.r WARNING @ Tue, 14 Jul 2020 10:54:35: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:54:35: #2 You may need to consider one of the other alternative d(s): 4,49,550 WARNING @ Tue, 14 Jul 2020 10:54:35: #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 10:54:35: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:54:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:54:38: 3000000 INFO @ Tue, 14 Jul 2020 10:54:45: 4000000 INFO @ Tue, 14 Jul 2020 10:54:49: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 10:54:51: 5000000 INFO @ Tue, 14 Jul 2020 10:54:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521320/SRX8521320.10_peaks.xls INFO @ Tue, 14 Jul 2020 10:54:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521320/SRX8521320.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:54:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521320/SRX8521320.10_summits.bed INFO @ Tue, 14 Jul 2020 10:54:56: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (560 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:54:58: 6000000 INFO @ Tue, 14 Jul 2020 10:55:04: #1 tag size is determined as 59 bps INFO @ Tue, 14 Jul 2020 10:55:04: #1 tag size = 59 INFO @ Tue, 14 Jul 2020 10:55:04: #1 total tags in treatment: 6890855 INFO @ Tue, 14 Jul 2020 10:55:04: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:55:04: #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 10:55:04: #1 tags after filtering in treatment: 6890855 INFO @ Tue, 14 Jul 2020 10:55:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:55:04: #1 finished! INFO @ Tue, 14 Jul 2020 10:55:04: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:55:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:55:04: #2 number of paired peaks: 304 WARNING @ Tue, 14 Jul 2020 10:55:04: Fewer paired peaks (304) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 304 pairs to build model! INFO @ Tue, 14 Jul 2020 10:55:04: start model_add_line... INFO @ Tue, 14 Jul 2020 10:55:04: start X-correlation... INFO @ Tue, 14 Jul 2020 10:55:04: end of X-cor INFO @ Tue, 14 Jul 2020 10:55:04: #2 finished! INFO @ Tue, 14 Jul 2020 10:55:04: #2 predicted fragment length is 49 bps INFO @ Tue, 14 Jul 2020 10:55:04: #2 alternative fragment length(s) may be 4,49,550 bps INFO @ Tue, 14 Jul 2020 10:55:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521320/SRX8521320.20_model.r WARNING @ Tue, 14 Jul 2020 10:55:04: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:55:04: #2 You may need to consider one of the other alternative d(s): 4,49,550 WARNING @ Tue, 14 Jul 2020 10:55:04: #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 10:55:04: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:55:04: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 10:55:18: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:55:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521320/SRX8521320.20_peaks.xls INFO @ Tue, 14 Jul 2020 10:55:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521320/SRX8521320.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:55:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521320/SRX8521320.20_summits.bed INFO @ Tue, 14 Jul 2020 10:55:25: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (110 records, 4 fields): 1 millis CompletedMACS2peakCalling