Job ID = 14170626 SRX = SRX9434464 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 36392751 spots for SRR12982862/SRR12982862.sra Written 36392751 spots for SRR12982862/SRR12982862.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171075 ("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: 00:14:29 36392751 reads; of these: 36392751 (100.00%) were unpaired; of these: 808773 (2.22%) aligned 0 times 24539499 (67.43%) aligned exactly 1 time 11044479 (30.35%) aligned >1 times 97.78% overall alignment rate Time searching: 00:14:29 Overall time: 00:14:29 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] 7744435 / 35583978 = 0.2176 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 07:58:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9434464/SRX9434464.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9434464/SRX9434464.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9434464/SRX9434464.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9434464/SRX9434464.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 07:58:11: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:58:11: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:58:17: 1000000 INFO @ Sat, 11 Dec 2021 07:58:22: 2000000 INFO @ Sat, 11 Dec 2021 07:58:28: 3000000 INFO @ Sat, 11 Dec 2021 07:58:33: 4000000 INFO @ Sat, 11 Dec 2021 07:58:39: 5000000 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 07:58:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9434464/SRX9434464.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9434464/SRX9434464.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9434464/SRX9434464.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9434464/SRX9434464.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 07:58:41: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:58:41: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:58:45: 6000000 INFO @ Sat, 11 Dec 2021 07:58:50: 1000000 INFO @ Sat, 11 Dec 2021 07:58:52: 7000000 INFO @ Sat, 11 Dec 2021 07:58:58: 8000000 INFO @ Sat, 11 Dec 2021 07:58:59: 2000000 INFO @ Sat, 11 Dec 2021 07:59:05: 9000000 INFO @ Sat, 11 Dec 2021 07:59:07: 3000000 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 07:59:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9434464/SRX9434464.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9434464/SRX9434464.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9434464/SRX9434464.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9434464/SRX9434464.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 07:59:11: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:59:11: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:59:12: 10000000 INFO @ Sat, 11 Dec 2021 07:59:16: 4000000 INFO @ Sat, 11 Dec 2021 07:59:18: 1000000 INFO @ Sat, 11 Dec 2021 07:59:19: 11000000 INFO @ Sat, 11 Dec 2021 07:59:24: 5000000 INFO @ Sat, 11 Dec 2021 07:59:25: 2000000 INFO @ Sat, 11 Dec 2021 07:59:25: 12000000 INFO @ Sat, 11 Dec 2021 07:59:32: 3000000 INFO @ Sat, 11 Dec 2021 07:59:32: 13000000 INFO @ Sat, 11 Dec 2021 07:59:33: 6000000 INFO @ Sat, 11 Dec 2021 07:59:38: 4000000 INFO @ Sat, 11 Dec 2021 07:59:39: 14000000 INFO @ Sat, 11 Dec 2021 07:59:42: 7000000 INFO @ Sat, 11 Dec 2021 07:59:45: 5000000 INFO @ Sat, 11 Dec 2021 07:59:46: 15000000 INFO @ Sat, 11 Dec 2021 07:59:50: 8000000 INFO @ Sat, 11 Dec 2021 07:59:52: 6000000 INFO @ Sat, 11 Dec 2021 07:59:53: 16000000 INFO @ Sat, 11 Dec 2021 07:59:59: 9000000 INFO @ Sat, 11 Dec 2021 07:59:59: 7000000 INFO @ Sat, 11 Dec 2021 07:59:59: 17000000 INFO @ Sat, 11 Dec 2021 08:00:06: 8000000 INFO @ Sat, 11 Dec 2021 08:00:06: 18000000 INFO @ Sat, 11 Dec 2021 08:00:08: 10000000 INFO @ Sat, 11 Dec 2021 08:00:13: 9000000 INFO @ Sat, 11 Dec 2021 08:00:13: 19000000 INFO @ Sat, 11 Dec 2021 08:00:17: 11000000 INFO @ Sat, 11 Dec 2021 08:00:20: 10000000 INFO @ Sat, 11 Dec 2021 08:00:20: 20000000 INFO @ Sat, 11 Dec 2021 08:00:25: 12000000 INFO @ Sat, 11 Dec 2021 08:00:26: 11000000 INFO @ Sat, 11 Dec 2021 08:00:27: 21000000 INFO @ Sat, 11 Dec 2021 08:00:33: 12000000 INFO @ Sat, 11 Dec 2021 08:00:34: 22000000 INFO @ Sat, 11 Dec 2021 08:00:34: 13000000 INFO @ Sat, 11 Dec 2021 08:00:40: 13000000 INFO @ Sat, 11 Dec 2021 08:00:41: 23000000 INFO @ Sat, 11 Dec 2021 08:00:43: 14000000 INFO @ Sat, 11 Dec 2021 08:00:47: 14000000 INFO @ Sat, 11 Dec 2021 08:00:48: 24000000 INFO @ Sat, 11 Dec 2021 08:00:52: 15000000 INFO @ Sat, 11 Dec 2021 08:00:54: 15000000 INFO @ Sat, 11 Dec 2021 08:00:55: 25000000 INFO @ Sat, 11 Dec 2021 08:01:01: 16000000 INFO @ Sat, 11 Dec 2021 08:01:01: 16000000 INFO @ Sat, 11 Dec 2021 08:01:02: 26000000 INFO @ Sat, 11 Dec 2021 08:01:08: 27000000 INFO @ Sat, 11 Dec 2021 08:01:10: 17000000 INFO @ Sat, 11 Dec 2021 08:01:10: 17000000 INFO @ Sat, 11 Dec 2021 08:01:14: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 08:01:14: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 08:01:14: #1 total tags in treatment: 27839543 INFO @ Sat, 11 Dec 2021 08:01:14: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:01:14: #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 08:01:15: #1 tags after filtering in treatment: 27839543 INFO @ Sat, 11 Dec 2021 08:01:15: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 08:01:15: #1 finished! INFO @ Sat, 11 Dec 2021 08:01:15: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:01:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:01:16: #2 number of paired peaks: 138 WARNING @ Sat, 11 Dec 2021 08:01:16: Fewer paired peaks (138) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 138 pairs to build model! INFO @ Sat, 11 Dec 2021 08:01:16: start model_add_line... INFO @ Sat, 11 Dec 2021 08:01:16: start X-correlation... INFO @ Sat, 11 Dec 2021 08:01:16: end of X-cor INFO @ Sat, 11 Dec 2021 08:01:16: #2 finished! INFO @ Sat, 11 Dec 2021 08:01:16: #2 predicted fragment length is 44 bps INFO @ Sat, 11 Dec 2021 08:01:16: #2 alternative fragment length(s) may be 1,44,456,476,594 bps INFO @ Sat, 11 Dec 2021 08:01:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9434464/SRX9434464.05_model.r WARNING @ Sat, 11 Dec 2021 08:01:17: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 08:01:17: #2 You may need to consider one of the other alternative d(s): 1,44,456,476,594 WARNING @ Sat, 11 Dec 2021 08:01:17: #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 08:01:17: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:01:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 08:01:17: 18000000 INFO @ Sat, 11 Dec 2021 08:01:19: 18000000 INFO @ Sat, 11 Dec 2021 08:01:24: 19000000 INFO @ Sat, 11 Dec 2021 08:01:28: 19000000 INFO @ Sat, 11 Dec 2021 08:01:31: 20000000 INFO @ Sat, 11 Dec 2021 08:01:37: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 08:01:38: 21000000 INFO @ Sat, 11 Dec 2021 08:01:45: 22000000 INFO @ Sat, 11 Dec 2021 08:01:46: 21000000 INFO @ Sat, 11 Dec 2021 08:01:52: 23000000 INFO @ Sat, 11 Dec 2021 08:01:54: 22000000 INFO @ Sat, 11 Dec 2021 08:01:59: 24000000 INFO @ Sat, 11 Dec 2021 08:02:02: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:02:03: 23000000 INFO @ Sat, 11 Dec 2021 08:02:06: 25000000 INFO @ Sat, 11 Dec 2021 08:02:11: 24000000 INFO @ Sat, 11 Dec 2021 08:02:13: 26000000 INFO @ Sat, 11 Dec 2021 08:02:20: 25000000 INFO @ Sat, 11 Dec 2021 08:02:20: 27000000 INFO @ Sat, 11 Dec 2021 08:02:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9434464/SRX9434464.05_peaks.xls INFO @ Sat, 11 Dec 2021 08:02:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9434464/SRX9434464.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:02:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9434464/SRX9434464.05_summits.bed INFO @ Sat, 11 Dec 2021 08:02:26: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2029 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 08:02:26: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 08:02:26: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 08:02:26: #1 total tags in treatment: 27839543 INFO @ Sat, 11 Dec 2021 08:02:26: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:02:26: #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 08:02:27: #1 tags after filtering in treatment: 27839543 INFO @ Sat, 11 Dec 2021 08:02:27: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 08:02:27: #1 finished! INFO @ Sat, 11 Dec 2021 08:02:27: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:02:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:02:28: 26000000 INFO @ Sat, 11 Dec 2021 08:02:29: #2 number of paired peaks: 138 WARNING @ Sat, 11 Dec 2021 08:02:29: Fewer paired peaks (138) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 138 pairs to build model! INFO @ Sat, 11 Dec 2021 08:02:29: start model_add_line... INFO @ Sat, 11 Dec 2021 08:02:29: start X-correlation... INFO @ Sat, 11 Dec 2021 08:02:29: end of X-cor INFO @ Sat, 11 Dec 2021 08:02:29: #2 finished! INFO @ Sat, 11 Dec 2021 08:02:29: #2 predicted fragment length is 44 bps INFO @ Sat, 11 Dec 2021 08:02:29: #2 alternative fragment length(s) may be 1,44,456,476,594 bps INFO @ Sat, 11 Dec 2021 08:02:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9434464/SRX9434464.20_model.r WARNING @ Sat, 11 Dec 2021 08:02:29: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 08:02:29: #2 You may need to consider one of the other alternative d(s): 1,44,456,476,594 WARNING @ Sat, 11 Dec 2021 08:02:29: #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 08:02:29: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:02:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 08:02:36: 27000000 INFO @ Sat, 11 Dec 2021 08:02:42: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 08:02:42: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 08:02:42: #1 total tags in treatment: 27839543 INFO @ Sat, 11 Dec 2021 08:02:42: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:02:42: #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 08:02:43: #1 tags after filtering in treatment: 27839543 INFO @ Sat, 11 Dec 2021 08:02:43: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 08:02:43: #1 finished! INFO @ Sat, 11 Dec 2021 08:02:43: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:02:43: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:02:45: #2 number of paired peaks: 138 WARNING @ Sat, 11 Dec 2021 08:02:45: Fewer paired peaks (138) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 138 pairs to build model! INFO @ Sat, 11 Dec 2021 08:02:45: start model_add_line... INFO @ Sat, 11 Dec 2021 08:02:45: start X-correlation... INFO @ Sat, 11 Dec 2021 08:02:45: end of X-cor INFO @ Sat, 11 Dec 2021 08:02:45: #2 finished! INFO @ Sat, 11 Dec 2021 08:02:45: #2 predicted fragment length is 44 bps INFO @ Sat, 11 Dec 2021 08:02:45: #2 alternative fragment length(s) may be 1,44,456,476,594 bps INFO @ Sat, 11 Dec 2021 08:02:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9434464/SRX9434464.10_model.r WARNING @ Sat, 11 Dec 2021 08:02:45: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 08:02:45: #2 You may need to consider one of the other alternative d(s): 1,44,456,476,594 WARNING @ Sat, 11 Dec 2021 08:02:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 08:02:45: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:02:45: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 08:03:14: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:03:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9434464/SRX9434464.20_peaks.xls INFO @ Sat, 11 Dec 2021 08:03:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9434464/SRX9434464.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:03:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9434464/SRX9434464.20_summits.bed INFO @ Sat, 11 Dec 2021 08:03:37: Done! pass1 - making usageList (8 chroms): 4 millis pass2 - checking and writing primary data (326 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 08:03:41: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:04:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9434464/SRX9434464.10_peaks.xls INFO @ Sat, 11 Dec 2021 08:04:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9434464/SRX9434464.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:04:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9434464/SRX9434464.10_summits.bed INFO @ Sat, 11 Dec 2021 08:04:08: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (735 records, 4 fields): 2 millis CompletedMACS2peakCalling