Job ID = 14172107 SRX = SRX9103812 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 25502833 spots for SRR12621012/SRR12621012.sra Written 25502833 spots for SRR12621012/SRR12621012.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172634 ("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: 00:25:08 25502833 reads; of these: 25502833 (100.00%) were paired; of these: 6717566 (26.34%) aligned concordantly 0 times 9288581 (36.42%) aligned concordantly exactly 1 time 9496686 (37.24%) aligned concordantly >1 times ---- 6717566 pairs aligned concordantly 0 times; of these: 1858949 (27.67%) aligned discordantly 1 time ---- 4858617 pairs aligned 0 times concordantly or discordantly; of these: 9717234 mates make up the pairs; of these: 6815943 (70.14%) aligned 0 times 706999 (7.28%) aligned exactly 1 time 2194292 (22.58%) aligned >1 times 86.64% overall alignment rate Time searching: 00:25:08 Overall time: 00:25:08 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_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 7468326 / 20369881 = 0.3666 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 14:51:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9103812/SRX9103812.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9103812/SRX9103812.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9103812/SRX9103812.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9103812/SRX9103812.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 14:51:55: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:51:55: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:51:59: 1000000 INFO @ Sat, 11 Dec 2021 14:52:04: 2000000 INFO @ Sat, 11 Dec 2021 14:52:08: 3000000 INFO @ Sat, 11 Dec 2021 14:52:13: 4000000 INFO @ Sat, 11 Dec 2021 14:52:17: 5000000 INFO @ Sat, 11 Dec 2021 14:52:22: 6000000 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 14:52:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9103812/SRX9103812.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9103812/SRX9103812.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9103812/SRX9103812.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9103812/SRX9103812.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 14:52:25: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:52:25: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:52:26: 7000000 INFO @ Sat, 11 Dec 2021 14:52:29: 1000000 INFO @ Sat, 11 Dec 2021 14:52:31: 8000000 INFO @ Sat, 11 Dec 2021 14:52:34: 2000000 INFO @ Sat, 11 Dec 2021 14:52:35: 9000000 INFO @ Sat, 11 Dec 2021 14:52:39: 3000000 INFO @ Sat, 11 Dec 2021 14:52:40: 10000000 INFO @ Sat, 11 Dec 2021 14:52:43: 4000000 INFO @ Sat, 11 Dec 2021 14:52:45: 11000000 INFO @ Sat, 11 Dec 2021 14:52:48: 5000000 INFO @ Sat, 11 Dec 2021 14:52:49: 12000000 INFO @ Sat, 11 Dec 2021 14:52:53: 6000000 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 14:52:54: 13000000 INFO @ Sat, 11 Dec 2021 14:52:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9103812/SRX9103812.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9103812/SRX9103812.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9103812/SRX9103812.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9103812/SRX9103812.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 14:52:55: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:52:55: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:52:57: 7000000 INFO @ Sat, 11 Dec 2021 14:52:59: 14000000 INFO @ Sat, 11 Dec 2021 14:53:00: 1000000 INFO @ Sat, 11 Dec 2021 14:53:02: 8000000 INFO @ Sat, 11 Dec 2021 14:53:04: 15000000 INFO @ Sat, 11 Dec 2021 14:53:04: 2000000 INFO @ Sat, 11 Dec 2021 14:53:07: 9000000 INFO @ Sat, 11 Dec 2021 14:53:08: 16000000 INFO @ Sat, 11 Dec 2021 14:53:09: 3000000 INFO @ Sat, 11 Dec 2021 14:53:12: 10000000 INFO @ Sat, 11 Dec 2021 14:53:13: 17000000 INFO @ Sat, 11 Dec 2021 14:53:14: 4000000 INFO @ Sat, 11 Dec 2021 14:53:16: 11000000 INFO @ Sat, 11 Dec 2021 14:53:17: 18000000 INFO @ Sat, 11 Dec 2021 14:53:18: 5000000 INFO @ Sat, 11 Dec 2021 14:53:21: 12000000 INFO @ Sat, 11 Dec 2021 14:53:22: 19000000 INFO @ Sat, 11 Dec 2021 14:53:23: 6000000 INFO @ Sat, 11 Dec 2021 14:53:26: 13000000 INFO @ Sat, 11 Dec 2021 14:53:26: 20000000 INFO @ Sat, 11 Dec 2021 14:53:28: 7000000 INFO @ Sat, 11 Dec 2021 14:53:30: 14000000 INFO @ Sat, 11 Dec 2021 14:53:30: 21000000 INFO @ Sat, 11 Dec 2021 14:53:33: 8000000 INFO @ Sat, 11 Dec 2021 14:53:35: 22000000 INFO @ Sat, 11 Dec 2021 14:53:35: 15000000 INFO @ Sat, 11 Dec 2021 14:53:38: 9000000 INFO @ Sat, 11 Dec 2021 14:53:39: 23000000 INFO @ Sat, 11 Dec 2021 14:53:40: 16000000 INFO @ Sat, 11 Dec 2021 14:53:42: 10000000 INFO @ Sat, 11 Dec 2021 14:53:44: 24000000 INFO @ Sat, 11 Dec 2021 14:53:44: 17000000 INFO @ Sat, 11 Dec 2021 14:53:47: 11000000 INFO @ Sat, 11 Dec 2021 14:53:49: 18000000 INFO @ Sat, 11 Dec 2021 14:53:49: 25000000 INFO @ Sat, 11 Dec 2021 14:53:52: 12000000 INFO @ Sat, 11 Dec 2021 14:53:53: 19000000 INFO @ Sat, 11 Dec 2021 14:53:54: 26000000 INFO @ Sat, 11 Dec 2021 14:53:56: 13000000 INFO @ Sat, 11 Dec 2021 14:53:57: 20000000 INFO @ Sat, 11 Dec 2021 14:53:58: 27000000 INFO @ Sat, 11 Dec 2021 14:54:01: 14000000 INFO @ Sat, 11 Dec 2021 14:54:02: 21000000 INFO @ Sat, 11 Dec 2021 14:54:03: 28000000 INFO @ Sat, 11 Dec 2021 14:54:06: 15000000 INFO @ Sat, 11 Dec 2021 14:54:06: 22000000 INFO @ Sat, 11 Dec 2021 14:54:08: 29000000 INFO @ Sat, 11 Dec 2021 14:54:09: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 14:54:09: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 14:54:09: #1 total tags in treatment: 11526144 INFO @ Sat, 11 Dec 2021 14:54:09: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:54:09: #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 14:54:09: #1 tags after filtering in treatment: 8801658 INFO @ Sat, 11 Dec 2021 14:54:09: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 11 Dec 2021 14:54:09: #1 finished! INFO @ Sat, 11 Dec 2021 14:54:09: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:54:09: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:54:10: #2 number of paired peaks: 669 WARNING @ Sat, 11 Dec 2021 14:54:10: Fewer paired peaks (669) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 669 pairs to build model! INFO @ Sat, 11 Dec 2021 14:54:10: start model_add_line... INFO @ Sat, 11 Dec 2021 14:54:10: start X-correlation... INFO @ Sat, 11 Dec 2021 14:54:10: end of X-cor INFO @ Sat, 11 Dec 2021 14:54:10: #2 finished! INFO @ Sat, 11 Dec 2021 14:54:10: #2 predicted fragment length is 67 bps INFO @ Sat, 11 Dec 2021 14:54:10: #2 alternative fragment length(s) may be 67 bps INFO @ Sat, 11 Dec 2021 14:54:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9103812/SRX9103812.05_model.r WARNING @ Sat, 11 Dec 2021 14:54:10: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:54:10: #2 You may need to consider one of the other alternative d(s): 67 WARNING @ Sat, 11 Dec 2021 14:54:10: #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 14:54:10: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:54:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:54:11: 16000000 INFO @ Sat, 11 Dec 2021 14:54:11: 23000000 INFO @ Sat, 11 Dec 2021 14:54:16: 17000000 INFO @ Sat, 11 Dec 2021 14:54:16: 24000000 INFO @ Sat, 11 Dec 2021 14:54:20: 18000000 INFO @ Sat, 11 Dec 2021 14:54:20: 25000000 INFO @ Sat, 11 Dec 2021 14:54:24: 19000000 INFO @ Sat, 11 Dec 2021 14:54:25: 26000000 INFO @ Sat, 11 Dec 2021 14:54:28: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:54:29: 20000000 INFO @ Sat, 11 Dec 2021 14:54:30: 27000000 INFO @ Sat, 11 Dec 2021 14:54:33: 21000000 INFO @ Sat, 11 Dec 2021 14:54:34: 28000000 INFO @ Sat, 11 Dec 2021 14:54:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9103812/SRX9103812.05_peaks.xls INFO @ Sat, 11 Dec 2021 14:54:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9103812/SRX9103812.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:54:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9103812/SRX9103812.05_summits.bed INFO @ Sat, 11 Dec 2021 14:54:37: Done! INFO @ Sat, 11 Dec 2021 14:54:37: 22000000 INFO @ Sat, 11 Dec 2021 14:54:39: 29000000 INFO @ Sat, 11 Dec 2021 14:54:40: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 14:54:40: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 14:54:40: #1 total tags in treatment: 11526144 INFO @ Sat, 11 Dec 2021 14:54:40: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:54:40: #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 14:54:41: #1 tags after filtering in treatment: 8801658 INFO @ Sat, 11 Dec 2021 14:54:41: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 11 Dec 2021 14:54:41: #1 finished! INFO @ Sat, 11 Dec 2021 14:54:41: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:54:41: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8177 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 14:54:41: #2 number of paired peaks: 669 WARNING @ Sat, 11 Dec 2021 14:54:41: Fewer paired peaks (669) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 669 pairs to build model! INFO @ Sat, 11 Dec 2021 14:54:41: start model_add_line... INFO @ Sat, 11 Dec 2021 14:54:41: start X-correlation... INFO @ Sat, 11 Dec 2021 14:54:41: end of X-cor INFO @ Sat, 11 Dec 2021 14:54:41: #2 finished! INFO @ Sat, 11 Dec 2021 14:54:41: #2 predicted fragment length is 67 bps INFO @ Sat, 11 Dec 2021 14:54:41: #2 alternative fragment length(s) may be 67 bps INFO @ Sat, 11 Dec 2021 14:54:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9103812/SRX9103812.10_model.r WARNING @ Sat, 11 Dec 2021 14:54:41: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:54:41: #2 You may need to consider one of the other alternative d(s): 67 WARNING @ Sat, 11 Dec 2021 14:54:41: #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 14:54:41: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:54:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:54:42: 23000000 INFO @ Sat, 11 Dec 2021 14:54:47: 24000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 14:54:51: 25000000 INFO @ Sat, 11 Dec 2021 14:54:56: 26000000 INFO @ Sat, 11 Dec 2021 14:54:59: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:55:00: 27000000 INFO @ Sat, 11 Dec 2021 14:55:05: 28000000 INFO @ Sat, 11 Dec 2021 14:55:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9103812/SRX9103812.10_peaks.xls INFO @ Sat, 11 Dec 2021 14:55:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9103812/SRX9103812.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:55:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9103812/SRX9103812.10_summits.bed INFO @ Sat, 11 Dec 2021 14:55:08: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3410 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 14:55:10: 29000000 INFO @ Sat, 11 Dec 2021 14:55:11: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 14:55:11: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 14:55:11: #1 total tags in treatment: 11526144 INFO @ Sat, 11 Dec 2021 14:55:11: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:55:11: #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 14:55:11: #1 tags after filtering in treatment: 8801658 INFO @ Sat, 11 Dec 2021 14:55:11: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 11 Dec 2021 14:55:11: #1 finished! INFO @ Sat, 11 Dec 2021 14:55:11: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:55:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:55:12: #2 number of paired peaks: 669 WARNING @ Sat, 11 Dec 2021 14:55:12: Fewer paired peaks (669) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 669 pairs to build model! INFO @ Sat, 11 Dec 2021 14:55:12: start model_add_line... INFO @ Sat, 11 Dec 2021 14:55:12: start X-correlation... INFO @ Sat, 11 Dec 2021 14:55:12: end of X-cor INFO @ Sat, 11 Dec 2021 14:55:12: #2 finished! INFO @ Sat, 11 Dec 2021 14:55:12: #2 predicted fragment length is 67 bps INFO @ Sat, 11 Dec 2021 14:55:12: #2 alternative fragment length(s) may be 67 bps INFO @ Sat, 11 Dec 2021 14:55:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9103812/SRX9103812.20_model.r WARNING @ Sat, 11 Dec 2021 14:55:12: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:55:12: #2 You may need to consider one of the other alternative d(s): 67 WARNING @ Sat, 11 Dec 2021 14:55:12: #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 14:55:12: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:55:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:55:29: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 14:55:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9103812/SRX9103812.20_peaks.xls INFO @ Sat, 11 Dec 2021 14:55:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9103812/SRX9103812.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:55:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9103812/SRX9103812.20_summits.bed INFO @ Sat, 11 Dec 2021 14:55:38: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (460 records, 4 fields): 1 millis CompletedMACS2peakCalling