Job ID = 14168447 SRX = ERX3978868 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 22869848 spots for ERR3975937/ERR3975937.sra Written 22869848 spots for ERR3975937/ERR3975937.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169840 ("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: 01:44:17 22869848 reads; of these: 22869848 (100.00%) were paired; of these: 3283236 (14.36%) aligned concordantly 0 times 12138318 (53.08%) aligned concordantly exactly 1 time 7448294 (32.57%) aligned concordantly >1 times ---- 3283236 pairs aligned concordantly 0 times; of these: 223144 (6.80%) aligned discordantly 1 time ---- 3060092 pairs aligned 0 times concordantly or discordantly; of these: 6120184 mates make up the pairs; of these: 2685240 (43.88%) aligned 0 times 1303233 (21.29%) aligned exactly 1 time 2131711 (34.83%) aligned >1 times 94.13% overall alignment rate Time searching: 01:44:17 Overall time: 01:44:17 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] 5586098 / 19687130 = 0.2837 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 20:27:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978868/ERX3978868.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978868/ERX3978868.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978868/ERX3978868.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978868/ERX3978868.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 20:27:35: #1 read tag files... INFO @ Fri, 10 Dec 2021 20:27:35: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 20:27:43: 1000000 INFO @ Fri, 10 Dec 2021 20:27:51: 2000000 INFO @ Fri, 10 Dec 2021 20:27:58: 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 20:28:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978868/ERX3978868.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978868/ERX3978868.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978868/ERX3978868.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978868/ERX3978868.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 20:28:05: #1 read tag files... INFO @ Fri, 10 Dec 2021 20:28:05: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 20:28:06: 4000000 INFO @ Fri, 10 Dec 2021 20:28:13: 1000000 INFO @ Fri, 10 Dec 2021 20:28:15: 5000000 INFO @ Fri, 10 Dec 2021 20:28:20: 2000000 INFO @ Fri, 10 Dec 2021 20:28:24: 6000000 INFO @ Fri, 10 Dec 2021 20:28:28: 3000000 INFO @ Fri, 10 Dec 2021 20:28:33: 7000000 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 20:28:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978868/ERX3978868.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978868/ERX3978868.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978868/ERX3978868.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978868/ERX3978868.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 20:28:35: #1 read tag files... INFO @ Fri, 10 Dec 2021 20:28:35: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 20:28:35: 4000000 INFO @ Fri, 10 Dec 2021 20:28:41: 8000000 INFO @ Fri, 10 Dec 2021 20:28:43: 1000000 INFO @ Fri, 10 Dec 2021 20:28:43: 5000000 INFO @ Fri, 10 Dec 2021 20:28:49: 9000000 INFO @ Fri, 10 Dec 2021 20:28:50: 2000000 INFO @ Fri, 10 Dec 2021 20:28:51: 6000000 INFO @ Fri, 10 Dec 2021 20:28:57: 10000000 INFO @ Fri, 10 Dec 2021 20:28:58: 3000000 INFO @ Fri, 10 Dec 2021 20:28:58: 7000000 INFO @ Fri, 10 Dec 2021 20:29:05: 11000000 INFO @ Fri, 10 Dec 2021 20:29:06: 4000000 INFO @ Fri, 10 Dec 2021 20:29:06: 8000000 INFO @ Fri, 10 Dec 2021 20:29:13: 5000000 INFO @ Fri, 10 Dec 2021 20:29:14: 12000000 INFO @ Fri, 10 Dec 2021 20:29:14: 9000000 INFO @ Fri, 10 Dec 2021 20:29:21: 6000000 INFO @ Fri, 10 Dec 2021 20:29:21: 10000000 INFO @ Fri, 10 Dec 2021 20:29:22: 13000000 INFO @ Fri, 10 Dec 2021 20:29:29: 7000000 INFO @ Fri, 10 Dec 2021 20:29:29: 11000000 INFO @ Fri, 10 Dec 2021 20:29:30: 14000000 INFO @ Fri, 10 Dec 2021 20:29:36: 8000000 INFO @ Fri, 10 Dec 2021 20:29:37: 12000000 INFO @ Fri, 10 Dec 2021 20:29:38: 15000000 INFO @ Fri, 10 Dec 2021 20:29:44: 9000000 INFO @ Fri, 10 Dec 2021 20:29:44: 13000000 INFO @ Fri, 10 Dec 2021 20:29:47: 16000000 INFO @ Fri, 10 Dec 2021 20:29:52: 10000000 INFO @ Fri, 10 Dec 2021 20:29:52: 14000000 INFO @ Fri, 10 Dec 2021 20:29:55: 17000000 INFO @ Fri, 10 Dec 2021 20:29:59: 11000000 INFO @ Fri, 10 Dec 2021 20:30:00: 15000000 INFO @ Fri, 10 Dec 2021 20:30:03: 18000000 INFO @ Fri, 10 Dec 2021 20:30:07: 12000000 INFO @ Fri, 10 Dec 2021 20:30:07: 16000000 INFO @ Fri, 10 Dec 2021 20:30:12: 19000000 INFO @ Fri, 10 Dec 2021 20:30:15: 13000000 INFO @ Fri, 10 Dec 2021 20:30:15: 17000000 INFO @ Fri, 10 Dec 2021 20:30:20: 20000000 INFO @ Fri, 10 Dec 2021 20:30:22: 14000000 INFO @ Fri, 10 Dec 2021 20:30:23: 18000000 INFO @ Fri, 10 Dec 2021 20:30:28: 21000000 INFO @ Fri, 10 Dec 2021 20:30:30: 15000000 INFO @ Fri, 10 Dec 2021 20:30:30: 19000000 INFO @ Fri, 10 Dec 2021 20:30:36: 22000000 INFO @ Fri, 10 Dec 2021 20:30:38: 16000000 INFO @ Fri, 10 Dec 2021 20:30:38: 20000000 INFO @ Fri, 10 Dec 2021 20:30:45: 23000000 INFO @ Fri, 10 Dec 2021 20:30:45: 17000000 INFO @ Fri, 10 Dec 2021 20:30:46: 21000000 INFO @ Fri, 10 Dec 2021 20:30:53: 18000000 INFO @ Fri, 10 Dec 2021 20:30:53: 22000000 INFO @ Fri, 10 Dec 2021 20:30:53: 24000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 20:31:00: 19000000 INFO @ Fri, 10 Dec 2021 20:31:01: 23000000 INFO @ Fri, 10 Dec 2021 20:31:02: 25000000 INFO @ Fri, 10 Dec 2021 20:31:08: 20000000 INFO @ Fri, 10 Dec 2021 20:31:09: 24000000 INFO @ Fri, 10 Dec 2021 20:31:11: 26000000 INFO @ Fri, 10 Dec 2021 20:31:15: 21000000 INFO @ Fri, 10 Dec 2021 20:31:16: 25000000 INFO @ Fri, 10 Dec 2021 20:31:19: 27000000 INFO @ Fri, 10 Dec 2021 20:31:23: 22000000 INFO @ Fri, 10 Dec 2021 20:31:24: 26000000 INFO @ Fri, 10 Dec 2021 20:31:28: 28000000 INFO @ Fri, 10 Dec 2021 20:31:31: 23000000 INFO @ Fri, 10 Dec 2021 20:31:31: 27000000 INFO @ Fri, 10 Dec 2021 20:31:36: 29000000 INFO @ Fri, 10 Dec 2021 20:31:38: 24000000 INFO @ Fri, 10 Dec 2021 20:31:39: 28000000 INFO @ Fri, 10 Dec 2021 20:31:45: 30000000 INFO @ Fri, 10 Dec 2021 20:31:46: 25000000 INFO @ Fri, 10 Dec 2021 20:31:46: 29000000 INFO @ Fri, 10 Dec 2021 20:31:53: 26000000 INFO @ Fri, 10 Dec 2021 20:31:53: 31000000 INFO @ Fri, 10 Dec 2021 20:31:54: 30000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 20:32:01: 27000000 INFO @ Fri, 10 Dec 2021 20:32:01: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 20:32:01: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 20:32:01: #1 total tags in treatment: 14017119 INFO @ Fri, 10 Dec 2021 20:32:01: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 20:32:01: #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 20:32:01: #1 tags after filtering in treatment: 12641361 INFO @ Fri, 10 Dec 2021 20:32:01: #1 Redundant rate of treatment: 0.10 INFO @ Fri, 10 Dec 2021 20:32:01: #1 finished! INFO @ Fri, 10 Dec 2021 20:32:01: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 20:32:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 20:32:01: 31000000 INFO @ Fri, 10 Dec 2021 20:32:02: #2 number of paired peaks: 276 WARNING @ Fri, 10 Dec 2021 20:32:02: Fewer paired peaks (276) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 276 pairs to build model! INFO @ Fri, 10 Dec 2021 20:32:02: start model_add_line... INFO @ Fri, 10 Dec 2021 20:32:02: start X-correlation... INFO @ Fri, 10 Dec 2021 20:32:02: end of X-cor INFO @ Fri, 10 Dec 2021 20:32:02: #2 finished! INFO @ Fri, 10 Dec 2021 20:32:02: #2 predicted fragment length is 128 bps INFO @ Fri, 10 Dec 2021 20:32:02: #2 alternative fragment length(s) may be 128 bps INFO @ Fri, 10 Dec 2021 20:32:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978868/ERX3978868.05_model.r WARNING @ Fri, 10 Dec 2021 20:32:02: #2 Since the d (128) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 20:32:02: #2 You may need to consider one of the other alternative d(s): 128 WARNING @ Fri, 10 Dec 2021 20:32:02: #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 20:32:02: #3 Call peaks... INFO @ Fri, 10 Dec 2021 20:32:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 20:32:08: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 20:32:08: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 20:32:08: #1 total tags in treatment: 14017119 INFO @ Fri, 10 Dec 2021 20:32:08: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 20:32:08: #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 20:32:08: 28000000 INFO @ Fri, 10 Dec 2021 20:32:08: #1 tags after filtering in treatment: 12641361 INFO @ Fri, 10 Dec 2021 20:32:08: #1 Redundant rate of treatment: 0.10 INFO @ Fri, 10 Dec 2021 20:32:08: #1 finished! INFO @ Fri, 10 Dec 2021 20:32:08: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 20:32:08: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 20:32:09: #2 number of paired peaks: 276 WARNING @ Fri, 10 Dec 2021 20:32:09: Fewer paired peaks (276) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 276 pairs to build model! INFO @ Fri, 10 Dec 2021 20:32:09: start model_add_line... INFO @ Fri, 10 Dec 2021 20:32:09: start X-correlation... INFO @ Fri, 10 Dec 2021 20:32:09: end of X-cor INFO @ Fri, 10 Dec 2021 20:32:09: #2 finished! INFO @ Fri, 10 Dec 2021 20:32:09: #2 predicted fragment length is 128 bps INFO @ Fri, 10 Dec 2021 20:32:09: #2 alternative fragment length(s) may be 128 bps INFO @ Fri, 10 Dec 2021 20:32:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978868/ERX3978868.10_model.r WARNING @ Fri, 10 Dec 2021 20:32:09: #2 Since the d (128) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 20:32:09: #2 You may need to consider one of the other alternative d(s): 128 WARNING @ Fri, 10 Dec 2021 20:32:09: #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 20:32:09: #3 Call peaks... INFO @ Fri, 10 Dec 2021 20:32:09: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 20:32:15: 29000000 INFO @ Fri, 10 Dec 2021 20:32:22: 30000000 INFO @ Fri, 10 Dec 2021 20:32:27: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 20:32:28: 31000000 INFO @ Fri, 10 Dec 2021 20:32:32: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 20:32:34: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 20:32:34: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 20:32:34: #1 total tags in treatment: 14017119 INFO @ Fri, 10 Dec 2021 20:32:34: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 20:32:34: #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 20:32:35: #1 tags after filtering in treatment: 12641361 INFO @ Fri, 10 Dec 2021 20:32:35: #1 Redundant rate of treatment: 0.10 INFO @ Fri, 10 Dec 2021 20:32:35: #1 finished! INFO @ Fri, 10 Dec 2021 20:32:35: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 20:32:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 20:32:35: #2 number of paired peaks: 276 WARNING @ Fri, 10 Dec 2021 20:32:35: Fewer paired peaks (276) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 276 pairs to build model! INFO @ Fri, 10 Dec 2021 20:32:35: start model_add_line... INFO @ Fri, 10 Dec 2021 20:32:35: start X-correlation... INFO @ Fri, 10 Dec 2021 20:32:36: end of X-cor INFO @ Fri, 10 Dec 2021 20:32:36: #2 finished! INFO @ Fri, 10 Dec 2021 20:32:36: #2 predicted fragment length is 128 bps INFO @ Fri, 10 Dec 2021 20:32:36: #2 alternative fragment length(s) may be 128 bps INFO @ Fri, 10 Dec 2021 20:32:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978868/ERX3978868.20_model.r WARNING @ Fri, 10 Dec 2021 20:32:36: #2 Since the d (128) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 20:32:36: #2 You may need to consider one of the other alternative d(s): 128 WARNING @ Fri, 10 Dec 2021 20:32:36: #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 20:32:36: #3 Call peaks... INFO @ Fri, 10 Dec 2021 20:32:36: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 20:32:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978868/ERX3978868.05_peaks.xls INFO @ Fri, 10 Dec 2021 20:32:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978868/ERX3978868.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 20:32:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978868/ERX3978868.05_summits.bed INFO @ Fri, 10 Dec 2021 20:32:41: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5321 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 20:32:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978868/ERX3978868.10_peaks.xls INFO @ Fri, 10 Dec 2021 20:32:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978868/ERX3978868.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 20:32:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978868/ERX3978868.10_summits.bed INFO @ Fri, 10 Dec 2021 20:32:45: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2671 records, 4 fields): 33 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 20:33:00: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 20:33:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978868/ERX3978868.20_peaks.xls INFO @ Fri, 10 Dec 2021 20:33:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978868/ERX3978868.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 20:33:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978868/ERX3978868.20_summits.bed INFO @ Fri, 10 Dec 2021 20:33:13: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1059 records, 4 fields): 3 millis CompletedMACS2peakCalling