Job ID = 14168379 SRX = ERX3978740 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 19807056 spots for ERR3975750/ERR3975750.sra Written 19807056 spots for ERR3975750/ERR3975750.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169691 ("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: 01:02:44 19807056 reads; of these: 19807056 (100.00%) were paired; of these: 6911165 (34.89%) aligned concordantly 0 times 5152036 (26.01%) aligned concordantly exactly 1 time 7743855 (39.10%) aligned concordantly >1 times ---- 6911165 pairs aligned concordantly 0 times; of these: 1677473 (24.27%) aligned discordantly 1 time ---- 5233692 pairs aligned 0 times concordantly or discordantly; of these: 10467384 mates make up the pairs; of these: 5949806 (56.84%) aligned 0 times 346612 (3.31%) aligned exactly 1 time 4170966 (39.85%) aligned >1 times 84.98% overall alignment rate Time searching: 01:02:44 Overall time: 01:02:44 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 24 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] 5866196 / 14477012 = 0.4052 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 19:31:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978740/ERX3978740.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978740/ERX3978740.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978740/ERX3978740.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978740/ERX3978740.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 19:31:48: #1 read tag files... INFO @ Fri, 10 Dec 2021 19:31:48: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 19:31:54: 1000000 INFO @ Fri, 10 Dec 2021 19:32:01: 2000000 INFO @ Fri, 10 Dec 2021 19:32:07: 3000000 INFO @ Fri, 10 Dec 2021 19:32:14: 4000000 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 19:32:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978740/ERX3978740.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978740/ERX3978740.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978740/ERX3978740.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978740/ERX3978740.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 19:32:17: #1 read tag files... INFO @ Fri, 10 Dec 2021 19:32:17: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 19:32:21: 5000000 INFO @ Fri, 10 Dec 2021 19:32:24: 1000000 INFO @ Fri, 10 Dec 2021 19:32:29: 6000000 INFO @ Fri, 10 Dec 2021 19:32:32: 2000000 INFO @ Fri, 10 Dec 2021 19:32:37: 7000000 INFO @ Fri, 10 Dec 2021 19:32:40: 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 19:32:44: 8000000 INFO @ Fri, 10 Dec 2021 19:32:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978740/ERX3978740.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978740/ERX3978740.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978740/ERX3978740.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978740/ERX3978740.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 19:32:47: #1 read tag files... INFO @ Fri, 10 Dec 2021 19:32:47: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 19:32:48: 4000000 INFO @ Fri, 10 Dec 2021 19:32:52: 9000000 INFO @ Fri, 10 Dec 2021 19:32:53: 1000000 INFO @ Fri, 10 Dec 2021 19:32:56: 5000000 INFO @ Fri, 10 Dec 2021 19:33:00: 2000000 INFO @ Fri, 10 Dec 2021 19:33:00: 10000000 INFO @ Fri, 10 Dec 2021 19:33:03: 6000000 INFO @ Fri, 10 Dec 2021 19:33:08: 11000000 INFO @ Fri, 10 Dec 2021 19:33:08: 3000000 INFO @ Fri, 10 Dec 2021 19:33:11: 7000000 INFO @ Fri, 10 Dec 2021 19:33:15: 4000000 INFO @ Fri, 10 Dec 2021 19:33:15: 12000000 INFO @ Fri, 10 Dec 2021 19:33:19: 8000000 INFO @ Fri, 10 Dec 2021 19:33:21: 5000000 INFO @ Fri, 10 Dec 2021 19:33:22: 13000000 INFO @ Fri, 10 Dec 2021 19:33:27: 9000000 INFO @ Fri, 10 Dec 2021 19:33:28: 6000000 INFO @ Fri, 10 Dec 2021 19:33:29: 14000000 INFO @ Fri, 10 Dec 2021 19:33:34: 7000000 INFO @ Fri, 10 Dec 2021 19:33:35: 10000000 INFO @ Fri, 10 Dec 2021 19:33:36: 15000000 INFO @ Fri, 10 Dec 2021 19:33:41: 8000000 INFO @ Fri, 10 Dec 2021 19:33:43: 11000000 INFO @ Fri, 10 Dec 2021 19:33:43: 16000000 INFO @ Fri, 10 Dec 2021 19:33:48: 9000000 INFO @ Fri, 10 Dec 2021 19:33:50: 17000000 INFO @ Fri, 10 Dec 2021 19:33:51: 12000000 INFO @ Fri, 10 Dec 2021 19:33:54: 10000000 INFO @ Fri, 10 Dec 2021 19:33:58: 18000000 INFO @ Fri, 10 Dec 2021 19:33:58: 13000000 INFO @ Fri, 10 Dec 2021 19:34:01: 11000000 INFO @ Fri, 10 Dec 2021 19:34:05: 14000000 INFO @ Fri, 10 Dec 2021 19:34:06: 19000000 INFO @ Fri, 10 Dec 2021 19:34:07: 12000000 INFO @ Fri, 10 Dec 2021 19:34:12: 15000000 INFO @ Fri, 10 Dec 2021 19:34:13: 13000000 INFO @ Fri, 10 Dec 2021 19:34:13: 20000000 INFO @ Fri, 10 Dec 2021 19:34:19: 14000000 INFO @ Fri, 10 Dec 2021 19:34:19: 16000000 INFO @ Fri, 10 Dec 2021 19:34:21: 21000000 INFO @ Fri, 10 Dec 2021 19:34:25: 15000000 INFO @ Fri, 10 Dec 2021 19:34:27: 17000000 INFO @ Fri, 10 Dec 2021 19:34:29: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 19:34:29: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 19:34:29: #1 total tags in treatment: 7129833 INFO @ Fri, 10 Dec 2021 19:34:29: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 19:34:29: #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 19:34:29: #1 tags after filtering in treatment: 4919825 INFO @ Fri, 10 Dec 2021 19:34:29: #1 Redundant rate of treatment: 0.31 INFO @ Fri, 10 Dec 2021 19:34:29: #1 finished! INFO @ Fri, 10 Dec 2021 19:34:29: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 19:34:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 19:34:30: #2 number of paired peaks: 5325 INFO @ Fri, 10 Dec 2021 19:34:30: start model_add_line... INFO @ Fri, 10 Dec 2021 19:34:30: start X-correlation... INFO @ Fri, 10 Dec 2021 19:34:30: end of X-cor INFO @ Fri, 10 Dec 2021 19:34:30: #2 finished! INFO @ Fri, 10 Dec 2021 19:34:30: #2 predicted fragment length is 214 bps INFO @ Fri, 10 Dec 2021 19:34:30: #2 alternative fragment length(s) may be 214 bps INFO @ Fri, 10 Dec 2021 19:34:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978740/ERX3978740.05_model.r WARNING @ Fri, 10 Dec 2021 19:34:30: #2 Since the d (214) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 19:34:30: #2 You may need to consider one of the other alternative d(s): 214 WARNING @ Fri, 10 Dec 2021 19:34:30: #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 19:34:30: #3 Call peaks... INFO @ Fri, 10 Dec 2021 19:34:30: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 19:34:31: 16000000 INFO @ Fri, 10 Dec 2021 19:34:33: 18000000 INFO @ Fri, 10 Dec 2021 19:34:37: 17000000 INFO @ Fri, 10 Dec 2021 19:34:40: 19000000 INFO @ Fri, 10 Dec 2021 19:34:43: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 19:34:44: 18000000 INFO @ Fri, 10 Dec 2021 19:34:47: 20000000 INFO @ Fri, 10 Dec 2021 19:34:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978740/ERX3978740.05_peaks.xls INFO @ Fri, 10 Dec 2021 19:34:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978740/ERX3978740.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 19:34:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978740/ERX3978740.05_summits.bed INFO @ Fri, 10 Dec 2021 19:34:50: Done! INFO @ Fri, 10 Dec 2021 19:34:50: 19000000 pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (10800 records, 4 fields): 36 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 19:34:54: 21000000 INFO @ Fri, 10 Dec 2021 19:34:57: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 19:35:01: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 19:35:01: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 19:35:01: #1 total tags in treatment: 7129833 INFO @ Fri, 10 Dec 2021 19:35:01: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 19:35:01: #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 19:35:01: #1 tags after filtering in treatment: 4919825 INFO @ Fri, 10 Dec 2021 19:35:01: #1 Redundant rate of treatment: 0.31 INFO @ Fri, 10 Dec 2021 19:35:01: #1 finished! INFO @ Fri, 10 Dec 2021 19:35:01: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 19:35:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 19:35:02: #2 number of paired peaks: 5325 INFO @ Fri, 10 Dec 2021 19:35:02: start model_add_line... INFO @ Fri, 10 Dec 2021 19:35:02: start X-correlation... INFO @ Fri, 10 Dec 2021 19:35:02: end of X-cor INFO @ Fri, 10 Dec 2021 19:35:02: #2 finished! INFO @ Fri, 10 Dec 2021 19:35:02: #2 predicted fragment length is 214 bps INFO @ Fri, 10 Dec 2021 19:35:02: #2 alternative fragment length(s) may be 214 bps INFO @ Fri, 10 Dec 2021 19:35:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978740/ERX3978740.10_model.r WARNING @ Fri, 10 Dec 2021 19:35:02: #2 Since the d (214) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 19:35:02: #2 You may need to consider one of the other alternative d(s): 214 WARNING @ Fri, 10 Dec 2021 19:35:02: #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 19:35:02: #3 Call peaks... INFO @ Fri, 10 Dec 2021 19:35:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 19:35:03: 21000000 INFO @ Fri, 10 Dec 2021 19:35:10: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 19:35:10: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 19:35:10: #1 total tags in treatment: 7129833 INFO @ Fri, 10 Dec 2021 19:35:10: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 19:35:10: #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 19:35:10: #1 tags after filtering in treatment: 4919825 INFO @ Fri, 10 Dec 2021 19:35:10: #1 Redundant rate of treatment: 0.31 INFO @ Fri, 10 Dec 2021 19:35:10: #1 finished! INFO @ Fri, 10 Dec 2021 19:35:10: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 19:35:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 19:35:10: #2 number of paired peaks: 5325 INFO @ Fri, 10 Dec 2021 19:35:10: start model_add_line... INFO @ Fri, 10 Dec 2021 19:35:10: start X-correlation... INFO @ Fri, 10 Dec 2021 19:35:10: end of X-cor INFO @ Fri, 10 Dec 2021 19:35:10: #2 finished! INFO @ Fri, 10 Dec 2021 19:35:10: #2 predicted fragment length is 214 bps INFO @ Fri, 10 Dec 2021 19:35:10: #2 alternative fragment length(s) may be 214 bps INFO @ Fri, 10 Dec 2021 19:35:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978740/ERX3978740.20_model.r WARNING @ Fri, 10 Dec 2021 19:35:10: #2 Since the d (214) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 19:35:10: #2 You may need to consider one of the other alternative d(s): 214 WARNING @ Fri, 10 Dec 2021 19:35:10: #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 19:35:10: #3 Call peaks... INFO @ Fri, 10 Dec 2021 19:35:10: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 19:35:15: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 19:35:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978740/ERX3978740.10_peaks.xls INFO @ Fri, 10 Dec 2021 19:35:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978740/ERX3978740.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 19:35:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978740/ERX3978740.10_summits.bed INFO @ Fri, 10 Dec 2021 19:35:22: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7089 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 19:35:23: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 19:35:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978740/ERX3978740.20_peaks.xls INFO @ Fri, 10 Dec 2021 19:35:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978740/ERX3978740.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 19:35:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978740/ERX3978740.20_summits.bed INFO @ Fri, 10 Dec 2021 19:35:30: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (3305 records, 4 fields): 6 millis CompletedMACS2peakCalling BigWig に変換しました。