Job ID = 14168949 SRX = SRX9910783 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 41274134 spots for SRR13498854/SRR13498854.sra Written 41274134 spots for SRR13498854/SRR13498854.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170106 ("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: 01:34:14 41274134 reads; of these: 41274134 (100.00%) were paired; of these: 15846629 (38.39%) aligned concordantly 0 times 17843394 (43.23%) aligned concordantly exactly 1 time 7584111 (18.37%) aligned concordantly >1 times ---- 15846629 pairs aligned concordantly 0 times; of these: 2650299 (16.72%) aligned discordantly 1 time ---- 13196330 pairs aligned 0 times concordantly or discordantly; of these: 26392660 mates make up the pairs; of these: 22096788 (83.72%) aligned 0 times 607845 (2.30%) aligned exactly 1 time 3688027 (13.97%) aligned >1 times 73.23% overall alignment rate Time searching: 01:34:14 Overall time: 01:34:14 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 44 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] 11325320 / 27888030 = 0.4061 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 00:03:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9910783/SRX9910783.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9910783/SRX9910783.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9910783/SRX9910783.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9910783/SRX9910783.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 00:03:26: #1 read tag files... INFO @ Sat, 11 Dec 2021 00:03:26: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 00:03:33: 1000000 INFO @ Sat, 11 Dec 2021 00:03:41: 2000000 INFO @ Sat, 11 Dec 2021 00:03:48: 3000000 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 00:03:55: 4000000 INFO @ Sat, 11 Dec 2021 00:03:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9910783/SRX9910783.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9910783/SRX9910783.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9910783/SRX9910783.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9910783/SRX9910783.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 00:03:56: #1 read tag files... INFO @ Sat, 11 Dec 2021 00:03:56: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 00:04:04: 5000000 INFO @ Sat, 11 Dec 2021 00:04:04: 1000000 INFO @ Sat, 11 Dec 2021 00:04:13: 6000000 INFO @ Sat, 11 Dec 2021 00:04:13: 2000000 INFO @ Sat, 11 Dec 2021 00:04:22: 7000000 INFO @ Sat, 11 Dec 2021 00:04:22: 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 00:04:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9910783/SRX9910783.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9910783/SRX9910783.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9910783/SRX9910783.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9910783/SRX9910783.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 00:04:26: #1 read tag files... INFO @ Sat, 11 Dec 2021 00:04:26: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 00:04:31: 8000000 INFO @ Sat, 11 Dec 2021 00:04:31: 4000000 INFO @ Sat, 11 Dec 2021 00:04:37: 1000000 INFO @ Sat, 11 Dec 2021 00:04:41: 9000000 INFO @ Sat, 11 Dec 2021 00:04:41: 5000000 INFO @ Sat, 11 Dec 2021 00:04:49: 2000000 INFO @ Sat, 11 Dec 2021 00:04:51: 10000000 INFO @ Sat, 11 Dec 2021 00:04:51: 6000000 INFO @ Sat, 11 Dec 2021 00:05:00: 3000000 INFO @ Sat, 11 Dec 2021 00:05:01: 11000000 INFO @ Sat, 11 Dec 2021 00:05:01: 7000000 INFO @ Sat, 11 Dec 2021 00:05:11: 12000000 INFO @ Sat, 11 Dec 2021 00:05:11: 8000000 INFO @ Sat, 11 Dec 2021 00:05:12: 4000000 INFO @ Sat, 11 Dec 2021 00:05:21: 13000000 INFO @ Sat, 11 Dec 2021 00:05:21: 9000000 INFO @ Sat, 11 Dec 2021 00:05:23: 5000000 INFO @ Sat, 11 Dec 2021 00:05:31: 14000000 INFO @ Sat, 11 Dec 2021 00:05:31: 10000000 INFO @ Sat, 11 Dec 2021 00:05:34: 6000000 INFO @ Sat, 11 Dec 2021 00:05:41: 15000000 INFO @ Sat, 11 Dec 2021 00:05:41: 11000000 INFO @ Sat, 11 Dec 2021 00:05:45: 7000000 INFO @ Sat, 11 Dec 2021 00:05:51: 16000000 INFO @ Sat, 11 Dec 2021 00:05:51: 12000000 INFO @ Sat, 11 Dec 2021 00:05:56: 8000000 INFO @ Sat, 11 Dec 2021 00:06:01: 17000000 INFO @ Sat, 11 Dec 2021 00:06:01: 13000000 INFO @ Sat, 11 Dec 2021 00:06:07: 9000000 INFO @ Sat, 11 Dec 2021 00:06:11: 18000000 INFO @ Sat, 11 Dec 2021 00:06:11: 14000000 INFO @ Sat, 11 Dec 2021 00:06:18: 10000000 INFO @ Sat, 11 Dec 2021 00:06:21: 19000000 INFO @ Sat, 11 Dec 2021 00:06:21: 15000000 INFO @ Sat, 11 Dec 2021 00:06:29: 11000000 INFO @ Sat, 11 Dec 2021 00:06:31: 20000000 INFO @ Sat, 11 Dec 2021 00:06:31: 16000000 INFO @ Sat, 11 Dec 2021 00:06:40: 12000000 INFO @ Sat, 11 Dec 2021 00:06:41: 21000000 INFO @ Sat, 11 Dec 2021 00:06:41: 17000000 INFO @ Sat, 11 Dec 2021 00:06:51: 13000000 INFO @ Sat, 11 Dec 2021 00:06:51: 22000000 INFO @ Sat, 11 Dec 2021 00:06:51: 18000000 INFO @ Sat, 11 Dec 2021 00:07:01: 23000000 INFO @ Sat, 11 Dec 2021 00:07:01: 19000000 INFO @ Sat, 11 Dec 2021 00:07:02: 14000000 INFO @ Sat, 11 Dec 2021 00:07:11: 24000000 INFO @ Sat, 11 Dec 2021 00:07:11: 20000000 INFO @ Sat, 11 Dec 2021 00:07:13: 15000000 INFO @ Sat, 11 Dec 2021 00:07:20: 25000000 INFO @ Sat, 11 Dec 2021 00:07:21: 21000000 INFO @ Sat, 11 Dec 2021 00:07:23: 16000000 INFO @ Sat, 11 Dec 2021 00:07:30: 26000000 INFO @ Sat, 11 Dec 2021 00:07:30: 22000000 INFO @ Sat, 11 Dec 2021 00:07:33: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 00:07:40: 27000000 INFO @ Sat, 11 Dec 2021 00:07:40: 23000000 INFO @ Sat, 11 Dec 2021 00:07:44: 18000000 INFO @ Sat, 11 Dec 2021 00:07:49: 28000000 INFO @ Sat, 11 Dec 2021 00:07:50: 24000000 INFO @ Sat, 11 Dec 2021 00:07:55: 19000000 INFO @ Sat, 11 Dec 2021 00:07:59: 29000000 INFO @ Sat, 11 Dec 2021 00:07:59: 25000000 INFO @ Sat, 11 Dec 2021 00:08:06: 20000000 INFO @ Sat, 11 Dec 2021 00:08:08: 30000000 INFO @ Sat, 11 Dec 2021 00:08:09: 26000000 INFO @ Sat, 11 Dec 2021 00:08:17: 21000000 INFO @ Sat, 11 Dec 2021 00:08:18: 31000000 INFO @ Sat, 11 Dec 2021 00:08:19: 27000000 INFO @ Sat, 11 Dec 2021 00:08:28: 28000000 INFO @ Sat, 11 Dec 2021 00:08:28: 32000000 INFO @ Sat, 11 Dec 2021 00:08:29: 22000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 00:08:38: 29000000 INFO @ Sat, 11 Dec 2021 00:08:38: 33000000 INFO @ Sat, 11 Dec 2021 00:08:40: 23000000 INFO @ Sat, 11 Dec 2021 00:08:48: 30000000 INFO @ Sat, 11 Dec 2021 00:08:48: 34000000 INFO @ Sat, 11 Dec 2021 00:08:51: 24000000 INFO @ Sat, 11 Dec 2021 00:08:58: 31000000 INFO @ Sat, 11 Dec 2021 00:08:58: 35000000 INFO @ Sat, 11 Dec 2021 00:09:02: 25000000 INFO @ Sat, 11 Dec 2021 00:09:08: 32000000 INFO @ Sat, 11 Dec 2021 00:09:08: 36000000 INFO @ Sat, 11 Dec 2021 00:09:13: 26000000 INFO @ Sat, 11 Dec 2021 00:09:18: 37000000 INFO @ Sat, 11 Dec 2021 00:09:18: 33000000 INFO @ Sat, 11 Dec 2021 00:09:25: 27000000 INFO @ Sat, 11 Dec 2021 00:09:26: #1 tag size is determined as 151 bps INFO @ Sat, 11 Dec 2021 00:09:26: #1 tag size = 151 INFO @ Sat, 11 Dec 2021 00:09:26: #1 total tags in treatment: 14941384 INFO @ Sat, 11 Dec 2021 00:09:26: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 00:09:26: #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 00:09:26: #1 tags after filtering in treatment: 12024331 INFO @ Sat, 11 Dec 2021 00:09:26: #1 Redundant rate of treatment: 0.20 INFO @ Sat, 11 Dec 2021 00:09:26: #1 finished! INFO @ Sat, 11 Dec 2021 00:09:26: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 00:09:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 00:09:27: #2 number of paired peaks: 167 WARNING @ Sat, 11 Dec 2021 00:09:27: Fewer paired peaks (167) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 167 pairs to build model! INFO @ Sat, 11 Dec 2021 00:09:27: start model_add_line... INFO @ Sat, 11 Dec 2021 00:09:27: start X-correlation... INFO @ Sat, 11 Dec 2021 00:09:27: end of X-cor INFO @ Sat, 11 Dec 2021 00:09:27: #2 finished! INFO @ Sat, 11 Dec 2021 00:09:27: #2 predicted fragment length is 196 bps INFO @ Sat, 11 Dec 2021 00:09:27: #2 alternative fragment length(s) may be 196 bps INFO @ Sat, 11 Dec 2021 00:09:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9910783/SRX9910783.05_model.r WARNING @ Sat, 11 Dec 2021 00:09:27: #2 Since the d (196) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 00:09:27: #2 You may need to consider one of the other alternative d(s): 196 WARNING @ Sat, 11 Dec 2021 00:09:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 00:09:27: #3 Call peaks... INFO @ Sat, 11 Dec 2021 00:09:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 00:09:28: 34000000 INFO @ Sat, 11 Dec 2021 00:09:36: 28000000 INFO @ Sat, 11 Dec 2021 00:09:38: 35000000 INFO @ Sat, 11 Dec 2021 00:09:47: 29000000 INFO @ Sat, 11 Dec 2021 00:09:47: 36000000 INFO @ Sat, 11 Dec 2021 00:09:51: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 00:09:56: 37000000 INFO @ Sat, 11 Dec 2021 00:09:58: 30000000 INFO @ Sat, 11 Dec 2021 00:10:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9910783/SRX9910783.05_peaks.xls INFO @ Sat, 11 Dec 2021 00:10:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9910783/SRX9910783.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 00:10:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9910783/SRX9910783.05_summits.bed INFO @ Sat, 11 Dec 2021 00:10:03: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4385 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 00:10:04: #1 tag size is determined as 151 bps INFO @ Sat, 11 Dec 2021 00:10:04: #1 tag size = 151 INFO @ Sat, 11 Dec 2021 00:10:04: #1 total tags in treatment: 14941384 INFO @ Sat, 11 Dec 2021 00:10:04: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 00:10:04: #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 00:10:04: #1 tags after filtering in treatment: 12024331 INFO @ Sat, 11 Dec 2021 00:10:04: #1 Redundant rate of treatment: 0.20 INFO @ Sat, 11 Dec 2021 00:10:04: #1 finished! INFO @ Sat, 11 Dec 2021 00:10:04: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 00:10:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 00:10:05: #2 number of paired peaks: 167 WARNING @ Sat, 11 Dec 2021 00:10:05: Fewer paired peaks (167) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 167 pairs to build model! INFO @ Sat, 11 Dec 2021 00:10:05: start model_add_line... INFO @ Sat, 11 Dec 2021 00:10:05: start X-correlation... INFO @ Sat, 11 Dec 2021 00:10:05: end of X-cor INFO @ Sat, 11 Dec 2021 00:10:05: #2 finished! INFO @ Sat, 11 Dec 2021 00:10:05: #2 predicted fragment length is 196 bps INFO @ Sat, 11 Dec 2021 00:10:05: #2 alternative fragment length(s) may be 196 bps INFO @ Sat, 11 Dec 2021 00:10:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9910783/SRX9910783.10_model.r WARNING @ Sat, 11 Dec 2021 00:10:05: #2 Since the d (196) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 00:10:05: #2 You may need to consider one of the other alternative d(s): 196 WARNING @ Sat, 11 Dec 2021 00:10:05: #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 00:10:05: #3 Call peaks... INFO @ Sat, 11 Dec 2021 00:10:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 00:10:09: 31000000 INFO @ Sat, 11 Dec 2021 00:10:19: 32000000 INFO @ Sat, 11 Dec 2021 00:10:29: 33000000 INFO @ Sat, 11 Dec 2021 00:10:30: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 00:10:38: 34000000 INFO @ Sat, 11 Dec 2021 00:10:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9910783/SRX9910783.10_peaks.xls INFO @ Sat, 11 Dec 2021 00:10:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9910783/SRX9910783.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 00:10:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9910783/SRX9910783.10_summits.bed INFO @ Sat, 11 Dec 2021 00:10:42: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1368 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 00:10:48: 35000000 INFO @ Sat, 11 Dec 2021 00:10:58: 36000000 INFO @ Sat, 11 Dec 2021 00:11:06: 37000000 INFO @ Sat, 11 Dec 2021 00:11:12: #1 tag size is determined as 151 bps INFO @ Sat, 11 Dec 2021 00:11:12: #1 tag size = 151 INFO @ Sat, 11 Dec 2021 00:11:12: #1 total tags in treatment: 14941384 INFO @ Sat, 11 Dec 2021 00:11:12: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 00:11:12: #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 00:11:12: #1 tags after filtering in treatment: 12024331 INFO @ Sat, 11 Dec 2021 00:11:12: #1 Redundant rate of treatment: 0.20 INFO @ Sat, 11 Dec 2021 00:11:12: #1 finished! INFO @ Sat, 11 Dec 2021 00:11:12: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 00:11:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 00:11:13: #2 number of paired peaks: 167 WARNING @ Sat, 11 Dec 2021 00:11:13: Fewer paired peaks (167) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 167 pairs to build model! INFO @ Sat, 11 Dec 2021 00:11:13: start model_add_line... INFO @ Sat, 11 Dec 2021 00:11:13: start X-correlation... INFO @ Sat, 11 Dec 2021 00:11:13: end of X-cor INFO @ Sat, 11 Dec 2021 00:11:13: #2 finished! INFO @ Sat, 11 Dec 2021 00:11:13: #2 predicted fragment length is 196 bps INFO @ Sat, 11 Dec 2021 00:11:13: #2 alternative fragment length(s) may be 196 bps INFO @ Sat, 11 Dec 2021 00:11:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9910783/SRX9910783.20_model.r WARNING @ Sat, 11 Dec 2021 00:11:13: #2 Since the d (196) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 00:11:13: #2 You may need to consider one of the other alternative d(s): 196 WARNING @ Sat, 11 Dec 2021 00:11:13: #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 00:11:13: #3 Call peaks... INFO @ Sat, 11 Dec 2021 00:11:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 00:11:36: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 00:11:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9910783/SRX9910783.20_peaks.xls INFO @ Sat, 11 Dec 2021 00:11:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9910783/SRX9910783.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 00:11:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9910783/SRX9910783.20_summits.bed INFO @ Sat, 11 Dec 2021 00:11:48: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (371 records, 4 fields): 2 millis CompletedMACS2peakCalling