Job ID = 14168256 SRX = ERX3978727 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 18870489 spots for ERR3975736/ERR3975736.sra Written 18870489 spots for ERR3975736/ERR3975736.sra Read 26362887 spots for ERR3975756/ERR3975756.sra Written 26362887 spots for ERR3975756/ERR3975756.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169461 ("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: 01:04:30 45233376 reads; of these: 45233376 (100.00%) were paired; of these: 19710366 (43.57%) aligned concordantly 0 times 4612382 (10.20%) aligned concordantly exactly 1 time 20910628 (46.23%) aligned concordantly >1 times ---- 19710366 pairs aligned concordantly 0 times; of these: 1713575 (8.69%) aligned discordantly 1 time ---- 17996791 pairs aligned 0 times concordantly or discordantly; of these: 35993582 mates make up the pairs; of these: 18033217 (50.10%) aligned 0 times 618431 (1.72%) aligned exactly 1 time 17341934 (48.18%) aligned >1 times 80.07% overall alignment rate Time searching: 01:04:30 Overall time: 01:04:30 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 52 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] 18830714 / 26913696 = 0.6997 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 @ Fri, 10 Dec 2021 18:02:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978727/ERX3978727.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978727/ERX3978727.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978727/ERX3978727.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978727/ERX3978727.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 @ Fri, 10 Dec 2021 18:02:05: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:02:05: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:02:13: 1000000 INFO @ Fri, 10 Dec 2021 18:02:20: 2000000 INFO @ Fri, 10 Dec 2021 18:02:28: 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 @ Fri, 10 Dec 2021 18:02:35: 4000000 INFO @ Fri, 10 Dec 2021 18:02:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978727/ERX3978727.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978727/ERX3978727.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978727/ERX3978727.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978727/ERX3978727.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 @ Fri, 10 Dec 2021 18:02:35: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:02:35: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:02:43: 5000000 INFO @ Fri, 10 Dec 2021 18:02:43: 1000000 INFO @ Fri, 10 Dec 2021 18:02:51: 6000000 INFO @ Fri, 10 Dec 2021 18:02:51: 2000000 INFO @ Fri, 10 Dec 2021 18:02:59: 7000000 INFO @ Fri, 10 Dec 2021 18:03:00: 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 @ Fri, 10 Dec 2021 18:03:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978727/ERX3978727.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978727/ERX3978727.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978727/ERX3978727.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978727/ERX3978727.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 @ Fri, 10 Dec 2021 18:03:05: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:03:05: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:03:07: 8000000 INFO @ Fri, 10 Dec 2021 18:03:08: 4000000 INFO @ Fri, 10 Dec 2021 18:03:13: 1000000 INFO @ Fri, 10 Dec 2021 18:03:15: 9000000 INFO @ Fri, 10 Dec 2021 18:03:16: 5000000 INFO @ Fri, 10 Dec 2021 18:03:21: 2000000 INFO @ Fri, 10 Dec 2021 18:03:23: 10000000 INFO @ Fri, 10 Dec 2021 18:03:24: 6000000 INFO @ Fri, 10 Dec 2021 18:03:30: 3000000 INFO @ Fri, 10 Dec 2021 18:03:30: 11000000 INFO @ Fri, 10 Dec 2021 18:03:32: 7000000 INFO @ Fri, 10 Dec 2021 18:03:37: 12000000 INFO @ Fri, 10 Dec 2021 18:03:38: 4000000 INFO @ Fri, 10 Dec 2021 18:03:40: 8000000 INFO @ Fri, 10 Dec 2021 18:03:45: 13000000 INFO @ Fri, 10 Dec 2021 18:03:45: 5000000 INFO @ Fri, 10 Dec 2021 18:03:48: 9000000 INFO @ Fri, 10 Dec 2021 18:03:53: 14000000 INFO @ Fri, 10 Dec 2021 18:03:54: 6000000 INFO @ Fri, 10 Dec 2021 18:03:56: 10000000 INFO @ Fri, 10 Dec 2021 18:04:01: 15000000 INFO @ Fri, 10 Dec 2021 18:04:02: 7000000 INFO @ Fri, 10 Dec 2021 18:04:04: 11000000 INFO @ Fri, 10 Dec 2021 18:04:08: 16000000 INFO @ Fri, 10 Dec 2021 18:04:10: 8000000 INFO @ Fri, 10 Dec 2021 18:04:12: 12000000 INFO @ Fri, 10 Dec 2021 18:04:16: 17000000 INFO @ Fri, 10 Dec 2021 18:04:18: 9000000 INFO @ Fri, 10 Dec 2021 18:04:20: 13000000 INFO @ Fri, 10 Dec 2021 18:04:24: 18000000 INFO @ Fri, 10 Dec 2021 18:04:26: 10000000 INFO @ Fri, 10 Dec 2021 18:04:27: 14000000 INFO @ Fri, 10 Dec 2021 18:04:32: 19000000 INFO @ Fri, 10 Dec 2021 18:04:32: 11000000 INFO @ Fri, 10 Dec 2021 18:04:35: 15000000 INFO @ Fri, 10 Dec 2021 18:04:39: 12000000 INFO @ Fri, 10 Dec 2021 18:04:39: 20000000 INFO @ Fri, 10 Dec 2021 18:04:42: 16000000 INFO @ Fri, 10 Dec 2021 18:04:45: 13000000 INFO @ Fri, 10 Dec 2021 18:04:47: 21000000 INFO @ Fri, 10 Dec 2021 18:04:50: 17000000 INFO @ Fri, 10 Dec 2021 18:04:52: 14000000 INFO @ Fri, 10 Dec 2021 18:04:55: 22000000 INFO @ Fri, 10 Dec 2021 18:04:57: 18000000 INFO @ Fri, 10 Dec 2021 18:04:58: 15000000 INFO @ Fri, 10 Dec 2021 18:05:03: 23000000 INFO @ Fri, 10 Dec 2021 18:05:04: 19000000 INFO @ Fri, 10 Dec 2021 18:05:05: 16000000 INFO @ Fri, 10 Dec 2021 18:05:10: 24000000 INFO @ Fri, 10 Dec 2021 18:05:12: 17000000 INFO @ Fri, 10 Dec 2021 18:05:12: 20000000 INFO @ Fri, 10 Dec 2021 18:05:18: 25000000 INFO @ Fri, 10 Dec 2021 18:05:18: 18000000 INFO @ Fri, 10 Dec 2021 18:05:19: 21000000 INFO @ Fri, 10 Dec 2021 18:05:25: 19000000 INFO @ Fri, 10 Dec 2021 18:05:26: 26000000 INFO @ Fri, 10 Dec 2021 18:05:27: 22000000 INFO @ Fri, 10 Dec 2021 18:05:31: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 18:05:33: 27000000 INFO @ Fri, 10 Dec 2021 18:05:34: 23000000 INFO @ Fri, 10 Dec 2021 18:05:37: 21000000 INFO @ Fri, 10 Dec 2021 18:05:40: 28000000 INFO @ Fri, 10 Dec 2021 18:05:42: 24000000 INFO @ Fri, 10 Dec 2021 18:05:44: 22000000 INFO @ Fri, 10 Dec 2021 18:05:48: 29000000 INFO @ Fri, 10 Dec 2021 18:05:49: 25000000 INFO @ Fri, 10 Dec 2021 18:05:50: 23000000 INFO @ Fri, 10 Dec 2021 18:05:55: 30000000 INFO @ Fri, 10 Dec 2021 18:05:56: 26000000 INFO @ Fri, 10 Dec 2021 18:05:57: 24000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 18:06:02: 31000000 INFO @ Fri, 10 Dec 2021 18:06:03: 25000000 INFO @ Fri, 10 Dec 2021 18:06:04: 27000000 INFO @ Fri, 10 Dec 2021 18:06:10: 26000000 INFO @ Fri, 10 Dec 2021 18:06:10: 32000000 INFO @ Fri, 10 Dec 2021 18:06:11: 28000000 INFO @ Fri, 10 Dec 2021 18:06:16: 27000000 INFO @ Fri, 10 Dec 2021 18:06:18: 33000000 INFO @ Fri, 10 Dec 2021 18:06:18: 29000000 INFO @ Fri, 10 Dec 2021 18:06:22: 28000000 INFO @ Fri, 10 Dec 2021 18:06:26: 30000000 INFO @ Fri, 10 Dec 2021 18:06:26: 34000000 INFO @ Fri, 10 Dec 2021 18:06:29: 29000000 INFO @ Fri, 10 Dec 2021 18:06:32: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 18:06:32: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 18:06:32: #1 total tags in treatment: 6915296 INFO @ Fri, 10 Dec 2021 18:06:32: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:06:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 18:06:32: #1 tags after filtering in treatment: 4721431 INFO @ Fri, 10 Dec 2021 18:06:32: #1 Redundant rate of treatment: 0.32 INFO @ Fri, 10 Dec 2021 18:06:32: #1 finished! INFO @ Fri, 10 Dec 2021 18:06:32: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:06:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:06:32: #2 number of paired peaks: 2186 INFO @ Fri, 10 Dec 2021 18:06:32: start model_add_line... INFO @ Fri, 10 Dec 2021 18:06:32: start X-correlation... INFO @ Fri, 10 Dec 2021 18:06:32: end of X-cor INFO @ Fri, 10 Dec 2021 18:06:32: #2 finished! INFO @ Fri, 10 Dec 2021 18:06:32: #2 predicted fragment length is 205 bps INFO @ Fri, 10 Dec 2021 18:06:32: #2 alternative fragment length(s) may be 205 bps INFO @ Fri, 10 Dec 2021 18:06:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978727/ERX3978727.05_model.r WARNING @ Fri, 10 Dec 2021 18:06:32: #2 Since the d (205) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 18:06:32: #2 You may need to consider one of the other alternative d(s): 205 WARNING @ Fri, 10 Dec 2021 18:06:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 18:06:32: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:06:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 18:06:33: 31000000 INFO @ Fri, 10 Dec 2021 18:06:35: 30000000 INFO @ Fri, 10 Dec 2021 18:06:41: 32000000 INFO @ Fri, 10 Dec 2021 18:06:41: 31000000 INFO @ Fri, 10 Dec 2021 18:06:43: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:06:48: 32000000 INFO @ Fri, 10 Dec 2021 18:06:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978727/ERX3978727.05_peaks.xls INFO @ Fri, 10 Dec 2021 18:06:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978727/ERX3978727.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:06:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978727/ERX3978727.05_summits.bed INFO @ Fri, 10 Dec 2021 18:06:48: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5750 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 18:06:49: 33000000 INFO @ Fri, 10 Dec 2021 18:06:55: 33000000 INFO @ Fri, 10 Dec 2021 18:06:57: 34000000 INFO @ Fri, 10 Dec 2021 18:07:02: 34000000 INFO @ Fri, 10 Dec 2021 18:07:03: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 18:07:03: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 18:07:03: #1 total tags in treatment: 6915296 INFO @ Fri, 10 Dec 2021 18:07:03: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:07:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 18:07:03: #1 tags after filtering in treatment: 4721431 INFO @ Fri, 10 Dec 2021 18:07:03: #1 Redundant rate of treatment: 0.32 INFO @ Fri, 10 Dec 2021 18:07:03: #1 finished! INFO @ Fri, 10 Dec 2021 18:07:03: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:07:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:07:03: #2 number of paired peaks: 2186 INFO @ Fri, 10 Dec 2021 18:07:03: start model_add_line... INFO @ Fri, 10 Dec 2021 18:07:04: start X-correlation... INFO @ Fri, 10 Dec 2021 18:07:04: end of X-cor INFO @ Fri, 10 Dec 2021 18:07:04: #2 finished! INFO @ Fri, 10 Dec 2021 18:07:04: #2 predicted fragment length is 205 bps INFO @ Fri, 10 Dec 2021 18:07:04: #2 alternative fragment length(s) may be 205 bps INFO @ Fri, 10 Dec 2021 18:07:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978727/ERX3978727.10_model.r WARNING @ Fri, 10 Dec 2021 18:07:04: #2 Since the d (205) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 18:07:04: #2 You may need to consider one of the other alternative d(s): 205 WARNING @ Fri, 10 Dec 2021 18:07:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 18:07:04: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:07:04: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 18:07:07: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 18:07:07: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 18:07:07: #1 total tags in treatment: 6915296 INFO @ Fri, 10 Dec 2021 18:07:07: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:07:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 18:07:07: #1 tags after filtering in treatment: 4721431 INFO @ Fri, 10 Dec 2021 18:07:07: #1 Redundant rate of treatment: 0.32 INFO @ Fri, 10 Dec 2021 18:07:07: #1 finished! INFO @ Fri, 10 Dec 2021 18:07:07: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:07:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:07:07: #2 number of paired peaks: 2186 INFO @ Fri, 10 Dec 2021 18:07:07: start model_add_line... INFO @ Fri, 10 Dec 2021 18:07:07: start X-correlation... INFO @ Fri, 10 Dec 2021 18:07:07: end of X-cor INFO @ Fri, 10 Dec 2021 18:07:07: #2 finished! INFO @ Fri, 10 Dec 2021 18:07:07: #2 predicted fragment length is 205 bps INFO @ Fri, 10 Dec 2021 18:07:07: #2 alternative fragment length(s) may be 205 bps INFO @ Fri, 10 Dec 2021 18:07:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978727/ERX3978727.20_model.r WARNING @ Fri, 10 Dec 2021 18:07:07: #2 Since the d (205) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 18:07:07: #2 You may need to consider one of the other alternative d(s): 205 WARNING @ Fri, 10 Dec 2021 18:07:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 18:07:07: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:07:07: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 18:07:14: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:07:17: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:07:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978727/ERX3978727.10_peaks.xls INFO @ Fri, 10 Dec 2021 18:07:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978727/ERX3978727.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:07:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978727/ERX3978727.10_summits.bed INFO @ Fri, 10 Dec 2021 18:07:20: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2796 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 18:07:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978727/ERX3978727.20_peaks.xls INFO @ Fri, 10 Dec 2021 18:07:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978727/ERX3978727.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:07:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978727/ERX3978727.20_summits.bed INFO @ Fri, 10 Dec 2021 18:07:22: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (835 records, 4 fields): 3 millis CompletedMACS2peakCalling