Job ID = 14172285 SRX = SRX3293001 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 29023113 spots for SRR6182827/SRR6182827.sra Written 29023113 spots for SRR6182827/SRR6182827.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172825 ("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: 00:14:33 29023113 reads; of these: 29023113 (100.00%) were unpaired; of these: 920530 (3.17%) aligned 0 times 23046708 (79.41%) aligned exactly 1 time 5055875 (17.42%) aligned >1 times 96.83% overall alignment rate Time searching: 00:14:33 Overall time: 00:14:33 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 12 files... [bam_rmdupse_core] 2443096 / 28102583 = 0.0869 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 15:28:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3293001/SRX3293001.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3293001/SRX3293001.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3293001/SRX3293001.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3293001/SRX3293001.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, 11 Dec 2021 15:28:38: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:28:38: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:28:48: 1000000 INFO @ Sat, 11 Dec 2021 15:28:58: 2000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 15:29:07: 3000000 INFO @ Sat, 11 Dec 2021 15:29:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3293001/SRX3293001.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3293001/SRX3293001.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3293001/SRX3293001.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3293001/SRX3293001.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, 11 Dec 2021 15:29:08: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:29:08: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:29:18: 4000000 INFO @ Sat, 11 Dec 2021 15:29:18: 1000000 INFO @ Sat, 11 Dec 2021 15:29:28: 5000000 INFO @ Sat, 11 Dec 2021 15:29:29: 2000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 15:29:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3293001/SRX3293001.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3293001/SRX3293001.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3293001/SRX3293001.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3293001/SRX3293001.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, 11 Dec 2021 15:29:38: #1 read tag files... INFO @ Sat, 11 Dec 2021 15:29:38: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 15:29:39: 6000000 INFO @ Sat, 11 Dec 2021 15:29:40: 3000000 INFO @ Sat, 11 Dec 2021 15:29:48: 1000000 INFO @ Sat, 11 Dec 2021 15:29:50: 7000000 INFO @ Sat, 11 Dec 2021 15:29:50: 4000000 INFO @ Sat, 11 Dec 2021 15:29:58: 2000000 INFO @ Sat, 11 Dec 2021 15:30:01: 8000000 INFO @ Sat, 11 Dec 2021 15:30:01: 5000000 INFO @ Sat, 11 Dec 2021 15:30:09: 3000000 INFO @ Sat, 11 Dec 2021 15:30:12: 9000000 INFO @ Sat, 11 Dec 2021 15:30:12: 6000000 INFO @ Sat, 11 Dec 2021 15:30:19: 4000000 INFO @ Sat, 11 Dec 2021 15:30:22: 10000000 INFO @ Sat, 11 Dec 2021 15:30:23: 7000000 INFO @ Sat, 11 Dec 2021 15:30:29: 5000000 INFO @ Sat, 11 Dec 2021 15:30:32: 11000000 INFO @ Sat, 11 Dec 2021 15:30:34: 8000000 INFO @ Sat, 11 Dec 2021 15:30:39: 6000000 INFO @ Sat, 11 Dec 2021 15:30:42: 12000000 INFO @ Sat, 11 Dec 2021 15:30:45: 9000000 INFO @ Sat, 11 Dec 2021 15:30:49: 7000000 INFO @ Sat, 11 Dec 2021 15:30:53: 13000000 INFO @ Sat, 11 Dec 2021 15:30:56: 10000000 INFO @ Sat, 11 Dec 2021 15:30:59: 8000000 INFO @ Sat, 11 Dec 2021 15:31:03: 14000000 INFO @ Sat, 11 Dec 2021 15:31:07: 11000000 INFO @ Sat, 11 Dec 2021 15:31:10: 9000000 INFO @ Sat, 11 Dec 2021 15:31:14: 15000000 INFO @ Sat, 11 Dec 2021 15:31:18: 12000000 INFO @ Sat, 11 Dec 2021 15:31:20: 10000000 INFO @ Sat, 11 Dec 2021 15:31:25: 16000000 INFO @ Sat, 11 Dec 2021 15:31:29: 13000000 INFO @ Sat, 11 Dec 2021 15:31:31: 11000000 INFO @ Sat, 11 Dec 2021 15:31:35: 17000000 INFO @ Sat, 11 Dec 2021 15:31:39: 14000000 INFO @ Sat, 11 Dec 2021 15:31:42: 12000000 INFO @ Sat, 11 Dec 2021 15:31:46: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 15:31:50: 15000000 INFO @ Sat, 11 Dec 2021 15:31:52: 13000000 INFO @ Sat, 11 Dec 2021 15:31:57: 19000000 INFO @ Sat, 11 Dec 2021 15:32:01: 16000000 INFO @ Sat, 11 Dec 2021 15:32:02: 14000000 INFO @ Sat, 11 Dec 2021 15:32:07: 20000000 INFO @ Sat, 11 Dec 2021 15:32:12: 17000000 INFO @ Sat, 11 Dec 2021 15:32:13: 15000000 INFO @ Sat, 11 Dec 2021 15:32:18: 21000000 INFO @ Sat, 11 Dec 2021 15:32:23: 18000000 INFO @ Sat, 11 Dec 2021 15:32:23: 16000000 INFO @ Sat, 11 Dec 2021 15:32:29: 22000000 INFO @ Sat, 11 Dec 2021 15:32:34: 19000000 INFO @ Sat, 11 Dec 2021 15:32:34: 17000000 INFO @ Sat, 11 Dec 2021 15:32:39: 23000000 INFO @ Sat, 11 Dec 2021 15:32:45: 20000000 INFO @ Sat, 11 Dec 2021 15:32:45: 18000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 15:32:50: 24000000 INFO @ Sat, 11 Dec 2021 15:32:55: 19000000 INFO @ Sat, 11 Dec 2021 15:32:55: 21000000 INFO @ Sat, 11 Dec 2021 15:33:00: 25000000 INFO @ Sat, 11 Dec 2021 15:33:06: 20000000 INFO @ Sat, 11 Dec 2021 15:33:06: 22000000 INFO @ Sat, 11 Dec 2021 15:33:07: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 15:33:07: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 15:33:07: #1 total tags in treatment: 25659487 INFO @ Sat, 11 Dec 2021 15:33:07: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:33:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 15:33:07: #1 tags after filtering in treatment: 25659487 INFO @ Sat, 11 Dec 2021 15:33:07: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 15:33:07: #1 finished! INFO @ Sat, 11 Dec 2021 15:33:07: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:33:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:33:09: #2 number of paired peaks: 122 WARNING @ Sat, 11 Dec 2021 15:33:09: Fewer paired peaks (122) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 122 pairs to build model! INFO @ Sat, 11 Dec 2021 15:33:09: start model_add_line... INFO @ Sat, 11 Dec 2021 15:33:09: start X-correlation... INFO @ Sat, 11 Dec 2021 15:33:09: end of X-cor INFO @ Sat, 11 Dec 2021 15:33:09: #2 finished! INFO @ Sat, 11 Dec 2021 15:33:09: #2 predicted fragment length is 99 bps INFO @ Sat, 11 Dec 2021 15:33:09: #2 alternative fragment length(s) may be 1,91,99,510,512,517,536,554,594,598 bps INFO @ Sat, 11 Dec 2021 15:33:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3293001/SRX3293001.05_model.r WARNING @ Sat, 11 Dec 2021 15:33:09: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 15:33:09: #2 You may need to consider one of the other alternative d(s): 1,91,99,510,512,517,536,554,594,598 WARNING @ Sat, 11 Dec 2021 15:33:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 15:33:09: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:33:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:33:16: 21000000 INFO @ Sat, 11 Dec 2021 15:33:17: 23000000 INFO @ Sat, 11 Dec 2021 15:33:26: 22000000 INFO @ Sat, 11 Dec 2021 15:33:27: 24000000 INFO @ Sat, 11 Dec 2021 15:33:37: 23000000 INFO @ Sat, 11 Dec 2021 15:33:37: 25000000 INFO @ Sat, 11 Dec 2021 15:33:44: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 15:33:44: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 15:33:44: #1 total tags in treatment: 25659487 INFO @ Sat, 11 Dec 2021 15:33:44: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:33:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 15:33:45: #1 tags after filtering in treatment: 25659487 INFO @ Sat, 11 Dec 2021 15:33:45: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 15:33:45: #1 finished! INFO @ Sat, 11 Dec 2021 15:33:45: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:33:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:33:46: #2 number of paired peaks: 122 WARNING @ Sat, 11 Dec 2021 15:33:46: Fewer paired peaks (122) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 122 pairs to build model! INFO @ Sat, 11 Dec 2021 15:33:46: start model_add_line... INFO @ Sat, 11 Dec 2021 15:33:46: start X-correlation... INFO @ Sat, 11 Dec 2021 15:33:46: end of X-cor INFO @ Sat, 11 Dec 2021 15:33:46: #2 finished! INFO @ Sat, 11 Dec 2021 15:33:46: #2 predicted fragment length is 99 bps INFO @ Sat, 11 Dec 2021 15:33:46: #2 alternative fragment length(s) may be 1,91,99,510,512,517,536,554,594,598 bps INFO @ Sat, 11 Dec 2021 15:33:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3293001/SRX3293001.10_model.r WARNING @ Sat, 11 Dec 2021 15:33:46: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 15:33:46: #2 You may need to consider one of the other alternative d(s): 1,91,99,510,512,517,536,554,594,598 WARNING @ Sat, 11 Dec 2021 15:33:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 15:33:46: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:33:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:33:47: 24000000 INFO @ Sat, 11 Dec 2021 15:33:52: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:33:56: 25000000 INFO @ Sat, 11 Dec 2021 15:34:02: #1 tag size is determined as 101 bps INFO @ Sat, 11 Dec 2021 15:34:02: #1 tag size = 101 INFO @ Sat, 11 Dec 2021 15:34:02: #1 total tags in treatment: 25659487 INFO @ Sat, 11 Dec 2021 15:34:02: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 15:34:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 15:34:03: #1 tags after filtering in treatment: 25659487 INFO @ Sat, 11 Dec 2021 15:34:03: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 15:34:03: #1 finished! INFO @ Sat, 11 Dec 2021 15:34:03: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 15:34:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 15:34:04: #2 number of paired peaks: 122 WARNING @ Sat, 11 Dec 2021 15:34:04: Fewer paired peaks (122) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 122 pairs to build model! INFO @ Sat, 11 Dec 2021 15:34:04: start model_add_line... INFO @ Sat, 11 Dec 2021 15:34:04: start X-correlation... INFO @ Sat, 11 Dec 2021 15:34:04: end of X-cor INFO @ Sat, 11 Dec 2021 15:34:04: #2 finished! INFO @ Sat, 11 Dec 2021 15:34:04: #2 predicted fragment length is 99 bps INFO @ Sat, 11 Dec 2021 15:34:04: #2 alternative fragment length(s) may be 1,91,99,510,512,517,536,554,594,598 bps INFO @ Sat, 11 Dec 2021 15:34:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3293001/SRX3293001.20_model.r WARNING @ Sat, 11 Dec 2021 15:34:04: #2 Since the d (99) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 15:34:04: #2 You may need to consider one of the other alternative d(s): 1,91,99,510,512,517,536,554,594,598 WARNING @ Sat, 11 Dec 2021 15:34:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 15:34:04: #3 Call peaks... INFO @ Sat, 11 Dec 2021 15:34:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 15:34:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3293001/SRX3293001.05_peaks.xls INFO @ Sat, 11 Dec 2021 15:34:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3293001/SRX3293001.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:34:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3293001/SRX3293001.05_summits.bed INFO @ Sat, 11 Dec 2021 15:34:13: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (966 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 15:34:28: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:34:48: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 15:34:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3293001/SRX3293001.10_peaks.xls INFO @ Sat, 11 Dec 2021 15:34:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3293001/SRX3293001.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:34:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3293001/SRX3293001.10_summits.bed INFO @ Sat, 11 Dec 2021 15:34:50: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (568 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 15:35:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3293001/SRX3293001.20_peaks.xls INFO @ Sat, 11 Dec 2021 15:35:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3293001/SRX3293001.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 15:35:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3293001/SRX3293001.20_summits.bed INFO @ Sat, 11 Dec 2021 15:35:09: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (255 records, 4 fields): 1 millis CompletedMACS2peakCalling