Job ID = 6626640 SRX = SRX7351003 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 18318892 spots for SRR10673633/SRR10673633.sra Written 18318892 spots for SRR10673633/SRR10673633.sra fastq に変換しました。 bowtie でマッピング中... Your job 6626777 ("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: 00:06:27 18318892 reads; of these: 18318892 (100.00%) were unpaired; of these: 820923 (4.48%) aligned 0 times 14304502 (78.09%) aligned exactly 1 time 3193467 (17.43%) aligned >1 times 95.52% overall alignment rate Time searching: 00:06:27 Overall time: 00:06:27 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] 2204815 / 17497969 = 0.1260 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 08:17:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7351003/SRX7351003.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7351003/SRX7351003.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7351003/SRX7351003.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7351003/SRX7351003.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 08:17:29: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:17:29: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:17:39: 1000000 INFO @ Tue, 14 Jul 2020 08:17:49: 2000000 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 08:17:58: 3000000 INFO @ Tue, 14 Jul 2020 08:18:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7351003/SRX7351003.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7351003/SRX7351003.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7351003/SRX7351003.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7351003/SRX7351003.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 08:18:00: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:18:00: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:18:06: 1000000 INFO @ Tue, 14 Jul 2020 08:18:07: 4000000 INFO @ Tue, 14 Jul 2020 08:18:13: 2000000 INFO @ Tue, 14 Jul 2020 08:18:17: 5000000 INFO @ Tue, 14 Jul 2020 08:18:20: 3000000 INFO @ Tue, 14 Jul 2020 08:18:26: 4000000 INFO @ Tue, 14 Jul 2020 08:18:27: 6000000 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 08:18:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7351003/SRX7351003.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7351003/SRX7351003.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7351003/SRX7351003.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7351003/SRX7351003.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 08:18:29: #1 read tag files... INFO @ Tue, 14 Jul 2020 08:18:29: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 08:18:33: 5000000 INFO @ Tue, 14 Jul 2020 08:18:37: 7000000 INFO @ Tue, 14 Jul 2020 08:18:37: 1000000 INFO @ Tue, 14 Jul 2020 08:18:40: 6000000 INFO @ Tue, 14 Jul 2020 08:18:45: 2000000 INFO @ Tue, 14 Jul 2020 08:18:46: 7000000 INFO @ Tue, 14 Jul 2020 08:18:47: 8000000 INFO @ Tue, 14 Jul 2020 08:18:53: 8000000 INFO @ Tue, 14 Jul 2020 08:18:53: 3000000 INFO @ Tue, 14 Jul 2020 08:18:55: 9000000 INFO @ Tue, 14 Jul 2020 08:19:00: 9000000 INFO @ Tue, 14 Jul 2020 08:19:01: 4000000 INFO @ Tue, 14 Jul 2020 08:19:02: 10000000 INFO @ Tue, 14 Jul 2020 08:19:07: 10000000 INFO @ Tue, 14 Jul 2020 08:19:09: 5000000 INFO @ Tue, 14 Jul 2020 08:19:10: 11000000 INFO @ Tue, 14 Jul 2020 08:19:13: 11000000 INFO @ Tue, 14 Jul 2020 08:19:16: 6000000 INFO @ Tue, 14 Jul 2020 08:19:17: 12000000 INFO @ Tue, 14 Jul 2020 08:19:20: 12000000 INFO @ Tue, 14 Jul 2020 08:19:24: 7000000 INFO @ Tue, 14 Jul 2020 08:19:25: 13000000 INFO @ Tue, 14 Jul 2020 08:19:27: 13000000 INFO @ Tue, 14 Jul 2020 08:19:32: 8000000 INFO @ Tue, 14 Jul 2020 08:19:32: 14000000 INFO @ Tue, 14 Jul 2020 08:19:34: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 08:19:39: 9000000 INFO @ Tue, 14 Jul 2020 08:19:39: 15000000 INFO @ Tue, 14 Jul 2020 08:19:41: 15000000 INFO @ Tue, 14 Jul 2020 08:19:42: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 08:19:42: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 08:19:42: #1 total tags in treatment: 15293154 INFO @ Tue, 14 Jul 2020 08:19:42: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:19:42: #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 08:19:42: #1 tags after filtering in treatment: 15293154 INFO @ Tue, 14 Jul 2020 08:19:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 08:19:42: #1 finished! INFO @ Tue, 14 Jul 2020 08:19:42: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:19:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:19:43: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 08:19:43: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 08:19:43: #1 total tags in treatment: 15293154 INFO @ Tue, 14 Jul 2020 08:19:43: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:19:43: #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 08:19:43: #2 number of paired peaks: 1317 INFO @ Tue, 14 Jul 2020 08:19:43: start model_add_line... INFO @ Tue, 14 Jul 2020 08:19:43: #1 tags after filtering in treatment: 15293154 INFO @ Tue, 14 Jul 2020 08:19:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 08:19:43: #1 finished! INFO @ Tue, 14 Jul 2020 08:19:43: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:19:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:19:43: start X-correlation... INFO @ Tue, 14 Jul 2020 08:19:43: end of X-cor INFO @ Tue, 14 Jul 2020 08:19:43: #2 finished! INFO @ Tue, 14 Jul 2020 08:19:43: #2 predicted fragment length is 129 bps INFO @ Tue, 14 Jul 2020 08:19:43: #2 alternative fragment length(s) may be 129 bps INFO @ Tue, 14 Jul 2020 08:19:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7351003/SRX7351003.05_model.r WARNING @ Tue, 14 Jul 2020 08:19:43: #2 Since the d (129) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:19:43: #2 You may need to consider one of the other alternative d(s): 129 WARNING @ Tue, 14 Jul 2020 08:19:43: #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 08:19:43: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:19:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:19:44: #2 number of paired peaks: 1317 INFO @ Tue, 14 Jul 2020 08:19:44: start model_add_line... INFO @ Tue, 14 Jul 2020 08:19:44: start X-correlation... INFO @ Tue, 14 Jul 2020 08:19:44: end of X-cor INFO @ Tue, 14 Jul 2020 08:19:44: #2 finished! INFO @ Tue, 14 Jul 2020 08:19:44: #2 predicted fragment length is 129 bps INFO @ Tue, 14 Jul 2020 08:19:44: #2 alternative fragment length(s) may be 129 bps INFO @ Tue, 14 Jul 2020 08:19:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7351003/SRX7351003.10_model.r WARNING @ Tue, 14 Jul 2020 08:19:44: #2 Since the d (129) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:19:44: #2 You may need to consider one of the other alternative d(s): 129 WARNING @ Tue, 14 Jul 2020 08:19:44: #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 08:19:44: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:19:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:19:47: 10000000 INFO @ Tue, 14 Jul 2020 08:19:54: 11000000 INFO @ Tue, 14 Jul 2020 08:20:01: 12000000 INFO @ Tue, 14 Jul 2020 08:20:08: 13000000 BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 08:20:15: 14000000 INFO @ Tue, 14 Jul 2020 08:20:16: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:20:18: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:20:24: 15000000 INFO @ Tue, 14 Jul 2020 08:20:26: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 08:20:26: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 08:20:26: #1 total tags in treatment: 15293154 INFO @ Tue, 14 Jul 2020 08:20:26: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 08:20:26: #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 08:20:26: #1 tags after filtering in treatment: 15293154 INFO @ Tue, 14 Jul 2020 08:20:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 08:20:26: #1 finished! INFO @ Tue, 14 Jul 2020 08:20:26: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 08:20:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 08:20:28: #2 number of paired peaks: 1317 INFO @ Tue, 14 Jul 2020 08:20:28: start model_add_line... INFO @ Tue, 14 Jul 2020 08:20:28: start X-correlation... INFO @ Tue, 14 Jul 2020 08:20:28: end of X-cor INFO @ Tue, 14 Jul 2020 08:20:28: #2 finished! INFO @ Tue, 14 Jul 2020 08:20:28: #2 predicted fragment length is 129 bps INFO @ Tue, 14 Jul 2020 08:20:28: #2 alternative fragment length(s) may be 129 bps INFO @ Tue, 14 Jul 2020 08:20:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7351003/SRX7351003.20_model.r WARNING @ Tue, 14 Jul 2020 08:20:28: #2 Since the d (129) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 08:20:28: #2 You may need to consider one of the other alternative d(s): 129 WARNING @ Tue, 14 Jul 2020 08:20:28: #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 08:20:28: #3 Call peaks... INFO @ Tue, 14 Jul 2020 08:20:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 08:20:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7351003/SRX7351003.05_peaks.xls INFO @ Tue, 14 Jul 2020 08:20:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7351003/SRX7351003.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:20:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7351003/SRX7351003.05_summits.bed INFO @ Tue, 14 Jul 2020 08:20:32: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (10142 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 08:20:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7351003/SRX7351003.10_peaks.xls INFO @ Tue, 14 Jul 2020 08:20:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7351003/SRX7351003.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:20:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7351003/SRX7351003.10_summits.bed INFO @ Tue, 14 Jul 2020 08:20:35: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (6476 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 08:21:00: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 08:21:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7351003/SRX7351003.20_peaks.xls INFO @ Tue, 14 Jul 2020 08:21:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7351003/SRX7351003.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 08:21:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7351003/SRX7351003.20_summits.bed INFO @ Tue, 14 Jul 2020 08:21:17: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2885 records, 4 fields): 4 millis CompletedMACS2peakCalling