Job ID = 12265297 SRX = SRX5010756 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 47498366 spots for SRR8191181/SRR8191181.sra Written 47498366 spots for SRR8191181/SRR8191181.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265473 ("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: 00:13:42 47498366 reads; of these: 47498366 (100.00%) were unpaired; of these: 1765785 (3.72%) aligned 0 times 22954813 (48.33%) aligned exactly 1 time 22777768 (47.95%) aligned >1 times 96.28% overall alignment rate Time searching: 00:13:42 Overall time: 00:13:42 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 20 files... [bam_rmdupse_core] 26799349 / 45732581 = 0.5860 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 06:49:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5010756/SRX5010756.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5010756/SRX5010756.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5010756/SRX5010756.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5010756/SRX5010756.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 06:49:57: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:49:57: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:50:04: 1000000 INFO @ Sat, 03 Apr 2021 06:50:10: 2000000 INFO @ Sat, 03 Apr 2021 06:50:16: 3000000 INFO @ Sat, 03 Apr 2021 06:50:23: 4000000 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 06:50:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5010756/SRX5010756.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5010756/SRX5010756.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5010756/SRX5010756.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5010756/SRX5010756.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 06:50:27: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:50:27: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:50:29: 5000000 INFO @ Sat, 03 Apr 2021 06:50:34: 1000000 INFO @ Sat, 03 Apr 2021 06:50:36: 6000000 INFO @ Sat, 03 Apr 2021 06:50:40: 2000000 INFO @ Sat, 03 Apr 2021 06:50:42: 7000000 INFO @ Sat, 03 Apr 2021 06:50:46: 3000000 INFO @ Sat, 03 Apr 2021 06:50:49: 8000000 INFO @ Sat, 03 Apr 2021 06:50:52: 4000000 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 06:50:56: 9000000 INFO @ Sat, 03 Apr 2021 06:50:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5010756/SRX5010756.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5010756/SRX5010756.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5010756/SRX5010756.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5010756/SRX5010756.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 06:50:57: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:50:57: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:50:59: 5000000 INFO @ Sat, 03 Apr 2021 06:51:03: 10000000 INFO @ Sat, 03 Apr 2021 06:51:04: 1000000 INFO @ Sat, 03 Apr 2021 06:51:05: 6000000 INFO @ Sat, 03 Apr 2021 06:51:09: 11000000 INFO @ Sat, 03 Apr 2021 06:51:10: 2000000 INFO @ Sat, 03 Apr 2021 06:51:11: 7000000 INFO @ Sat, 03 Apr 2021 06:51:16: 12000000 INFO @ Sat, 03 Apr 2021 06:51:16: 3000000 INFO @ Sat, 03 Apr 2021 06:51:17: 8000000 INFO @ Sat, 03 Apr 2021 06:51:23: 4000000 INFO @ Sat, 03 Apr 2021 06:51:23: 13000000 INFO @ Sat, 03 Apr 2021 06:51:24: 9000000 INFO @ Sat, 03 Apr 2021 06:51:29: 5000000 INFO @ Sat, 03 Apr 2021 06:51:30: 14000000 INFO @ Sat, 03 Apr 2021 06:51:30: 10000000 INFO @ Sat, 03 Apr 2021 06:51:35: 6000000 INFO @ Sat, 03 Apr 2021 06:51:36: 11000000 INFO @ Sat, 03 Apr 2021 06:51:36: 15000000 INFO @ Sat, 03 Apr 2021 06:51:41: 7000000 INFO @ Sat, 03 Apr 2021 06:51:42: 12000000 INFO @ Sat, 03 Apr 2021 06:51:43: 16000000 INFO @ Sat, 03 Apr 2021 06:51:48: 8000000 INFO @ Sat, 03 Apr 2021 06:51:49: 13000000 INFO @ Sat, 03 Apr 2021 06:51:50: 17000000 INFO @ Sat, 03 Apr 2021 06:51:54: 9000000 INFO @ Sat, 03 Apr 2021 06:51:55: 14000000 INFO @ Sat, 03 Apr 2021 06:51:56: 18000000 INFO @ Sat, 03 Apr 2021 06:52:00: 10000000 INFO @ Sat, 03 Apr 2021 06:52:01: 15000000 INFO @ Sat, 03 Apr 2021 06:52:02: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 06:52:02: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 06:52:02: #1 total tags in treatment: 18933232 INFO @ Sat, 03 Apr 2021 06:52:02: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:52:02: #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 06:52:03: #1 tags after filtering in treatment: 18933232 INFO @ Sat, 03 Apr 2021 06:52:03: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:52:03: #1 finished! INFO @ Sat, 03 Apr 2021 06:52:03: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:52:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:52:04: #2 number of paired peaks: 162 WARNING @ Sat, 03 Apr 2021 06:52:04: Fewer paired peaks (162) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 162 pairs to build model! INFO @ Sat, 03 Apr 2021 06:52:04: start model_add_line... INFO @ Sat, 03 Apr 2021 06:52:04: start X-correlation... INFO @ Sat, 03 Apr 2021 06:52:04: end of X-cor INFO @ Sat, 03 Apr 2021 06:52:04: #2 finished! INFO @ Sat, 03 Apr 2021 06:52:04: #2 predicted fragment length is 49 bps INFO @ Sat, 03 Apr 2021 06:52:04: #2 alternative fragment length(s) may be 4,37,49 bps INFO @ Sat, 03 Apr 2021 06:52:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5010756/SRX5010756.05_model.r WARNING @ Sat, 03 Apr 2021 06:52:04: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:52:04: #2 You may need to consider one of the other alternative d(s): 4,37,49 WARNING @ Sat, 03 Apr 2021 06:52:04: #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 06:52:04: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:52:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:52:06: 11000000 INFO @ Sat, 03 Apr 2021 06:52:08: 16000000 INFO @ Sat, 03 Apr 2021 06:52:12: 12000000 INFO @ Sat, 03 Apr 2021 06:52:14: 17000000 INFO @ Sat, 03 Apr 2021 06:52:18: 13000000 INFO @ Sat, 03 Apr 2021 06:52:20: 18000000 INFO @ Sat, 03 Apr 2021 06:52:24: 14000000 INFO @ Sat, 03 Apr 2021 06:52:25: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 06:52:25: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 06:52:25: #1 total tags in treatment: 18933232 INFO @ Sat, 03 Apr 2021 06:52:25: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:52:25: #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 06:52:26: #1 tags after filtering in treatment: 18933232 INFO @ Sat, 03 Apr 2021 06:52:26: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:52:26: #1 finished! INFO @ Sat, 03 Apr 2021 06:52:26: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:52:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:52:27: #2 number of paired peaks: 162 WARNING @ Sat, 03 Apr 2021 06:52:27: Fewer paired peaks (162) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 162 pairs to build model! INFO @ Sat, 03 Apr 2021 06:52:27: start model_add_line... INFO @ Sat, 03 Apr 2021 06:52:27: start X-correlation... INFO @ Sat, 03 Apr 2021 06:52:27: end of X-cor INFO @ Sat, 03 Apr 2021 06:52:27: #2 finished! INFO @ Sat, 03 Apr 2021 06:52:27: #2 predicted fragment length is 49 bps INFO @ Sat, 03 Apr 2021 06:52:27: #2 alternative fragment length(s) may be 4,37,49 bps INFO @ Sat, 03 Apr 2021 06:52:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5010756/SRX5010756.10_model.r WARNING @ Sat, 03 Apr 2021 06:52:27: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:52:27: #2 You may need to consider one of the other alternative d(s): 4,37,49 WARNING @ Sat, 03 Apr 2021 06:52:27: #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 06:52:27: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:52:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:52:30: 15000000 INFO @ Sat, 03 Apr 2021 06:52:36: 16000000 INFO @ Sat, 03 Apr 2021 06:52:41: 17000000 INFO @ Sat, 03 Apr 2021 06:52:43: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:52:47: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:52:52: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 06:52:52: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 06:52:52: #1 total tags in treatment: 18933232 INFO @ Sat, 03 Apr 2021 06:52:52: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:52:52: #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 06:52:52: #1 tags after filtering in treatment: 18933232 INFO @ Sat, 03 Apr 2021 06:52:52: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:52:52: #1 finished! INFO @ Sat, 03 Apr 2021 06:52:52: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:52:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:52:53: #2 number of paired peaks: 162 WARNING @ Sat, 03 Apr 2021 06:52:53: Fewer paired peaks (162) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 162 pairs to build model! INFO @ Sat, 03 Apr 2021 06:52:53: start model_add_line... INFO @ Sat, 03 Apr 2021 06:52:53: start X-correlation... INFO @ Sat, 03 Apr 2021 06:52:53: end of X-cor INFO @ Sat, 03 Apr 2021 06:52:53: #2 finished! INFO @ Sat, 03 Apr 2021 06:52:53: #2 predicted fragment length is 49 bps INFO @ Sat, 03 Apr 2021 06:52:53: #2 alternative fragment length(s) may be 4,37,49 bps INFO @ Sat, 03 Apr 2021 06:52:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5010756/SRX5010756.20_model.r WARNING @ Sat, 03 Apr 2021 06:52:54: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:52:54: #2 You may need to consider one of the other alternative d(s): 4,37,49 WARNING @ Sat, 03 Apr 2021 06:52:54: #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 06:52:54: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:52:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:53:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5010756/SRX5010756.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:53:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5010756/SRX5010756.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:53:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5010756/SRX5010756.05_summits.bed INFO @ Sat, 03 Apr 2021 06:53:04: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (8271 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:53:07: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:53:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5010756/SRX5010756.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:53:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5010756/SRX5010756.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:53:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5010756/SRX5010756.10_summits.bed INFO @ Sat, 03 Apr 2021 06:53:28: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3587 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:53:31: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 06:53:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5010756/SRX5010756.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:53:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5010756/SRX5010756.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:53:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5010756/SRX5010756.20_summits.bed INFO @ Sat, 03 Apr 2021 06:53:50: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (598 records, 4 fields): 2 millis CompletedMACS2peakCalling