Job ID = 12265304 SRX = SRX5010763 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 34488251 spots for SRR8191188/SRR8191188.sra Written 34488251 spots for SRR8191188/SRR8191188.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265490 ("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: 00:13:53 34488251 reads; of these: 34488251 (100.00%) were unpaired; of these: 2161006 (6.27%) aligned 0 times 19081629 (55.33%) aligned exactly 1 time 13245616 (38.41%) aligned >1 times 93.73% overall alignment rate Time searching: 00:13:53 Overall time: 00:13:53 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 16 files... [bam_rmdupse_core] 16362354 / 32327245 = 0.5061 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:53:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5010763/SRX5010763.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5010763/SRX5010763.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5010763/SRX5010763.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5010763/SRX5010763.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 @ Sat, 03 Apr 2021 06:53:41: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:53:41: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:53:49: 1000000 INFO @ Sat, 03 Apr 2021 06:53:58: 2000000 INFO @ Sat, 03 Apr 2021 06:54:06: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:54:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5010763/SRX5010763.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5010763/SRX5010763.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5010763/SRX5010763.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5010763/SRX5010763.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 @ Sat, 03 Apr 2021 06:54:11: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:54:11: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:54:15: 4000000 INFO @ Sat, 03 Apr 2021 06:54:20: 1000000 INFO @ Sat, 03 Apr 2021 06:54:24: 5000000 INFO @ Sat, 03 Apr 2021 06:54:30: 2000000 INFO @ Sat, 03 Apr 2021 06:54:33: 6000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:54:39: 3000000 INFO @ Sat, 03 Apr 2021 06:54:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5010763/SRX5010763.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5010763/SRX5010763.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5010763/SRX5010763.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5010763/SRX5010763.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 @ Sat, 03 Apr 2021 06:54:41: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:54:41: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:54:43: 7000000 INFO @ Sat, 03 Apr 2021 06:54:49: 4000000 INFO @ Sat, 03 Apr 2021 06:54:53: 1000000 INFO @ Sat, 03 Apr 2021 06:54:54: 8000000 INFO @ Sat, 03 Apr 2021 06:54:58: 5000000 INFO @ Sat, 03 Apr 2021 06:55:05: 2000000 INFO @ Sat, 03 Apr 2021 06:55:05: 9000000 INFO @ Sat, 03 Apr 2021 06:55:08: 6000000 INFO @ Sat, 03 Apr 2021 06:55:16: 3000000 INFO @ Sat, 03 Apr 2021 06:55:16: 10000000 INFO @ Sat, 03 Apr 2021 06:55:18: 7000000 INFO @ Sat, 03 Apr 2021 06:55:27: 11000000 INFO @ Sat, 03 Apr 2021 06:55:27: 4000000 INFO @ Sat, 03 Apr 2021 06:55:28: 8000000 INFO @ Sat, 03 Apr 2021 06:55:38: 9000000 INFO @ Sat, 03 Apr 2021 06:55:38: 12000000 INFO @ Sat, 03 Apr 2021 06:55:39: 5000000 INFO @ Sat, 03 Apr 2021 06:55:47: 10000000 INFO @ Sat, 03 Apr 2021 06:55:49: 13000000 INFO @ Sat, 03 Apr 2021 06:55:50: 6000000 INFO @ Sat, 03 Apr 2021 06:55:57: 11000000 INFO @ Sat, 03 Apr 2021 06:56:00: 14000000 INFO @ Sat, 03 Apr 2021 06:56:02: 7000000 INFO @ Sat, 03 Apr 2021 06:56:07: 12000000 INFO @ Sat, 03 Apr 2021 06:56:11: 15000000 INFO @ Sat, 03 Apr 2021 06:56:13: 8000000 INFO @ Sat, 03 Apr 2021 06:56:16: 13000000 INFO @ Sat, 03 Apr 2021 06:56:21: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 06:56:21: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 06:56:21: #1 total tags in treatment: 15964891 INFO @ Sat, 03 Apr 2021 06:56:21: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:56:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:56:22: #1 tags after filtering in treatment: 15964891 INFO @ Sat, 03 Apr 2021 06:56:22: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:56:22: #1 finished! INFO @ Sat, 03 Apr 2021 06:56:22: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:56:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:56:23: #2 number of paired peaks: 147 WARNING @ Sat, 03 Apr 2021 06:56:23: Fewer paired peaks (147) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 147 pairs to build model! INFO @ Sat, 03 Apr 2021 06:56:23: start model_add_line... INFO @ Sat, 03 Apr 2021 06:56:23: start X-correlation... INFO @ Sat, 03 Apr 2021 06:56:23: end of X-cor INFO @ Sat, 03 Apr 2021 06:56:23: #2 finished! INFO @ Sat, 03 Apr 2021 06:56:23: #2 predicted fragment length is 39 bps INFO @ Sat, 03 Apr 2021 06:56:23: #2 alternative fragment length(s) may be 2,39 bps INFO @ Sat, 03 Apr 2021 06:56:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5010763/SRX5010763.05_model.r WARNING @ Sat, 03 Apr 2021 06:56:23: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:56:23: #2 You may need to consider one of the other alternative d(s): 2,39 WARNING @ Sat, 03 Apr 2021 06:56:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:56:23: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:56:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:56:24: 9000000 INFO @ Sat, 03 Apr 2021 06:56:26: 14000000 INFO @ Sat, 03 Apr 2021 06:56:33: 10000000 INFO @ Sat, 03 Apr 2021 06:56:34: 15000000 INFO @ Sat, 03 Apr 2021 06:56:43: 11000000 INFO @ Sat, 03 Apr 2021 06:56:43: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 06:56:43: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 06:56:43: #1 total tags in treatment: 15964891 INFO @ Sat, 03 Apr 2021 06:56:43: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:56:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:56:44: #1 tags after filtering in treatment: 15964891 INFO @ Sat, 03 Apr 2021 06:56:44: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:56:44: #1 finished! INFO @ Sat, 03 Apr 2021 06:56:44: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:56:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:56:45: #2 number of paired peaks: 147 WARNING @ Sat, 03 Apr 2021 06:56:45: Fewer paired peaks (147) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 147 pairs to build model! INFO @ Sat, 03 Apr 2021 06:56:45: start model_add_line... INFO @ Sat, 03 Apr 2021 06:56:45: start X-correlation... INFO @ Sat, 03 Apr 2021 06:56:45: end of X-cor INFO @ Sat, 03 Apr 2021 06:56:45: #2 finished! INFO @ Sat, 03 Apr 2021 06:56:45: #2 predicted fragment length is 39 bps INFO @ Sat, 03 Apr 2021 06:56:45: #2 alternative fragment length(s) may be 2,39 bps INFO @ Sat, 03 Apr 2021 06:56:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5010763/SRX5010763.10_model.r WARNING @ Sat, 03 Apr 2021 06:56:45: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:56:45: #2 You may need to consider one of the other alternative d(s): 2,39 WARNING @ Sat, 03 Apr 2021 06:56:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:56:45: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:56:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:56:52: 12000000 INFO @ Sat, 03 Apr 2021 06:57:01: 13000000 INFO @ Sat, 03 Apr 2021 06:57:08: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:57:11: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:57:20: 15000000 INFO @ Sat, 03 Apr 2021 06:57:29: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 06:57:29: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 06:57:29: #1 total tags in treatment: 15964891 INFO @ Sat, 03 Apr 2021 06:57:29: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:57:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:57:29: #1 tags after filtering in treatment: 15964891 INFO @ Sat, 03 Apr 2021 06:57:29: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:57:29: #1 finished! INFO @ Sat, 03 Apr 2021 06:57:29: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:57:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:57:30: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:57:31: #2 number of paired peaks: 147 WARNING @ Sat, 03 Apr 2021 06:57:31: Fewer paired peaks (147) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 147 pairs to build model! INFO @ Sat, 03 Apr 2021 06:57:31: start model_add_line... INFO @ Sat, 03 Apr 2021 06:57:31: start X-correlation... INFO @ Sat, 03 Apr 2021 06:57:31: end of X-cor INFO @ Sat, 03 Apr 2021 06:57:31: #2 finished! INFO @ Sat, 03 Apr 2021 06:57:31: #2 predicted fragment length is 39 bps INFO @ Sat, 03 Apr 2021 06:57:31: #2 alternative fragment length(s) may be 2,39 bps INFO @ Sat, 03 Apr 2021 06:57:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5010763/SRX5010763.20_model.r WARNING @ Sat, 03 Apr 2021 06:57:31: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:57:31: #2 You may need to consider one of the other alternative d(s): 2,39 WARNING @ Sat, 03 Apr 2021 06:57:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:57:31: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:57:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:57:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5010763/SRX5010763.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:57:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5010763/SRX5010763.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:57:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5010763/SRX5010763.05_summits.bed INFO @ Sat, 03 Apr 2021 06:57:32: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (3814 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:57:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5010763/SRX5010763.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:57:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5010763/SRX5010763.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:57:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5010763/SRX5010763.10_summits.bed INFO @ Sat, 03 Apr 2021 06:57:55: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1211 records, 4 fields): 8 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 06:58:15: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:58:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5010763/SRX5010763.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:58:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5010763/SRX5010763.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:58:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5010763/SRX5010763.20_summits.bed INFO @ Sat, 03 Apr 2021 06:58:39: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (114 records, 4 fields): 3 millis CompletedMACS2peakCalling