Job ID = 6626694 SRX = SRX7351009 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 16987695 spots for SRR10673639/SRR10673639.sra Written 16987695 spots for SRR10673639/SRR10673639.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626963 ("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 16987695 reads; of these: 16987695 (100.00%) were unpaired; of these: 576634 (3.39%) aligned 0 times 13287206 (78.22%) aligned exactly 1 time 3123855 (18.39%) aligned >1 times 96.61% 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_sort_core] merging from 8 files... [bam_rmdupse_core] 2281652 / 16411061 = 0.1390 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 08:32:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7351009/SRX7351009.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7351009/SRX7351009.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7351009/SRX7351009.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7351009/SRX7351009.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 08:32:19: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:32:19: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:32:26: 1000000 INFO @ Tue, 14 Jul 2020 08:32:32: 2000000 INFO @ Tue, 14 Jul 2020 08:32:39: 3000000 INFO @ Tue, 14 Jul 2020 08:32:45: 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 08:32:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7351009/SRX7351009.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7351009/SRX7351009.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7351009/SRX7351009.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7351009/SRX7351009.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 08:32:49: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:32:49: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:32:51: 5000000 INFO @ Tue, 14 Jul 2020 08:32:57: 1000000 INFO @ Tue, 14 Jul 2020 08:32:57: 6000000 INFO @ Tue, 14 Jul 2020 08:33:04: 2000000 INFO @ Tue, 14 Jul 2020 08:33:04: 7000000 INFO @ Tue, 14 Jul 2020 08:33:10: 8000000 INFO @ Tue, 14 Jul 2020 08:33:11: 3000000 INFO @ Tue, 14 Jul 2020 08:33:17: 9000000 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 08:33:18: 4000000 INFO @ Tue, 14 Jul 2020 08:33:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7351009/SRX7351009.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7351009/SRX7351009.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7351009/SRX7351009.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7351009/SRX7351009.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 08:33:19: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:33:19: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:33:23: 10000000 INFO @ Tue, 14 Jul 2020 08:33:25: 5000000 INFO @ Tue, 14 Jul 2020 08:33:26: 1000000 INFO @ Tue, 14 Jul 2020 08:33:30: 11000000 INFO @ Tue, 14 Jul 2020 08:33:32: 6000000 INFO @ Tue, 14 Jul 2020 08:33:34: 2000000 INFO @ Tue, 14 Jul 2020 08:33:36: 12000000 INFO @ Tue, 14 Jul 2020 08:33:39: 7000000 INFO @ Tue, 14 Jul 2020 08:33:41: 3000000 INFO @ Tue, 14 Jul 2020 08:33:43: 13000000 INFO @ Tue, 14 Jul 2020 08:33:46: 8000000 INFO @ Tue, 14 Jul 2020 08:33:48: 4000000 INFO @ Tue, 14 Jul 2020 08:33:49: 14000000 INFO @ Tue, 14 Jul 2020 08:33:50: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 08:33:50: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 08:33:50: #1 total tags in treatment: 14129409 INFO @ Tue, 14 Jul 2020 08:33:50: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:33:50: #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 08:33:50: #1 tags after filtering in treatment: 14129409 INFO @ Tue, 14 Jul 2020 08:33:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 08:33:50: #1 finished! INFO @ Tue, 14 Jul 2020 08:33:50: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:33:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:33:51: #2 number of paired peaks: 2061 INFO @ Tue, 14 Jul 2020 08:33:51: start model_add_line... INFO @ Tue, 14 Jul 2020 08:33:51: start X-correlation... INFO @ Tue, 14 Jul 2020 08:33:51: end of X-cor INFO @ Tue, 14 Jul 2020 08:33:51: #2 finished! INFO @ Tue, 14 Jul 2020 08:33:51: #2 predicted fragment length is 128 bps INFO @ Tue, 14 Jul 2020 08:33:51: #2 alternative fragment length(s) may be 128 bps INFO @ Tue, 14 Jul 2020 08:33:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7351009/SRX7351009.05_model.r WARNING @ Tue, 14 Jul 2020 08:33:51: #2 Since the d (128) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:33:51: #2 You may need to consider one of the other alternative d(s): 128 WARNING @ Tue, 14 Jul 2020 08:33:51: #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 08:33:51: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:33:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:33:53: 9000000 INFO @ Tue, 14 Jul 2020 08:33:55: 5000000 INFO @ Tue, 14 Jul 2020 08:34:00: 10000000 INFO @ Tue, 14 Jul 2020 08:34:02: 6000000 INFO @ Tue, 14 Jul 2020 08:34:07: 11000000 INFO @ Tue, 14 Jul 2020 08:34:09: 7000000 INFO @ Tue, 14 Jul 2020 08:34:14: 12000000 INFO @ Tue, 14 Jul 2020 08:34:16: 8000000 INFO @ Tue, 14 Jul 2020 08:34:21: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 08:34:23: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:34:23: 9000000 INFO @ Tue, 14 Jul 2020 08:34:28: 14000000 INFO @ Tue, 14 Jul 2020 08:34:29: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 08:34:29: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 08:34:29: #1 total tags in treatment: 14129409 INFO @ Tue, 14 Jul 2020 08:34:29: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:34:29: #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 08:34:29: #1 tags after filtering in treatment: 14129409 INFO @ Tue, 14 Jul 2020 08:34:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 08:34:29: #1 finished! INFO @ Tue, 14 Jul 2020 08:34:29: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:34:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:34:30: 10000000 INFO @ Tue, 14 Jul 2020 08:34:30: #2 number of paired peaks: 2061 INFO @ Tue, 14 Jul 2020 08:34:30: start model_add_line... INFO @ Tue, 14 Jul 2020 08:34:30: start X-correlation... INFO @ Tue, 14 Jul 2020 08:34:30: end of X-cor INFO @ Tue, 14 Jul 2020 08:34:30: #2 finished! INFO @ Tue, 14 Jul 2020 08:34:30: #2 predicted fragment length is 128 bps INFO @ Tue, 14 Jul 2020 08:34:30: #2 alternative fragment length(s) may be 128 bps INFO @ Tue, 14 Jul 2020 08:34:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7351009/SRX7351009.10_model.r WARNING @ Tue, 14 Jul 2020 08:34:30: #2 Since the d (128) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:34:30: #2 You may need to consider one of the other alternative d(s): 128 WARNING @ Tue, 14 Jul 2020 08:34:30: #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 08:34:30: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:34:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:34:37: 11000000 INFO @ Tue, 14 Jul 2020 08:34:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7351009/SRX7351009.05_peaks.xls INFO @ Tue, 14 Jul 2020 08:34:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7351009/SRX7351009.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:34:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7351009/SRX7351009.05_summits.bed INFO @ Tue, 14 Jul 2020 08:34:38: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (11858 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 08:34:43: 12000000 BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 08:34:50: 13000000 INFO @ Tue, 14 Jul 2020 08:34:57: 14000000 INFO @ Tue, 14 Jul 2020 08:34:58: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 08:34:58: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 08:34:58: #1 total tags in treatment: 14129409 INFO @ Tue, 14 Jul 2020 08:34:58: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:34:58: #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 08:34:58: #1 tags after filtering in treatment: 14129409 INFO @ Tue, 14 Jul 2020 08:34:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 08:34:58: #1 finished! INFO @ Tue, 14 Jul 2020 08:34:58: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:34:58: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:34:59: #2 number of paired peaks: 2061 INFO @ Tue, 14 Jul 2020 08:34:59: start model_add_line... INFO @ Tue, 14 Jul 2020 08:34:59: start X-correlation... INFO @ Tue, 14 Jul 2020 08:34:59: end of X-cor INFO @ Tue, 14 Jul 2020 08:34:59: #2 finished! INFO @ Tue, 14 Jul 2020 08:34:59: #2 predicted fragment length is 128 bps INFO @ Tue, 14 Jul 2020 08:34:59: #2 alternative fragment length(s) may be 128 bps INFO @ Tue, 14 Jul 2020 08:34:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7351009/SRX7351009.20_model.r WARNING @ Tue, 14 Jul 2020 08:34:59: #2 Since the d (128) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:34:59: #2 You may need to consider one of the other alternative d(s): 128 WARNING @ Tue, 14 Jul 2020 08:34:59: #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 08:34:59: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:34:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:35:02: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:35:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7351009/SRX7351009.10_peaks.xls INFO @ Tue, 14 Jul 2020 08:35:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7351009/SRX7351009.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:35:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7351009/SRX7351009.10_summits.bed INFO @ Tue, 14 Jul 2020 08:35:17: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (7289 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 08:35:31: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:35:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7351009/SRX7351009.20_peaks.xls INFO @ Tue, 14 Jul 2020 08:35:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7351009/SRX7351009.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:35:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7351009/SRX7351009.20_summits.bed INFO @ Tue, 14 Jul 2020 08:35:46: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3008 records, 4 fields): 4 millis CompletedMACS2peakCalling