Job ID = 14168436 SRX = ERX3978865 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 25648474 spots for ERR3975934/ERR3975934.sra Written 25648474 spots for ERR3975934/ERR3975934.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169853 ("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: 02:05:51 25648474 reads; of these: 25648474 (100.00%) were paired; of these: 3984927 (15.54%) aligned concordantly 0 times 13592189 (52.99%) aligned concordantly exactly 1 time 8071358 (31.47%) aligned concordantly >1 times ---- 3984927 pairs aligned concordantly 0 times; of these: 347812 (8.73%) aligned discordantly 1 time ---- 3637115 pairs aligned 0 times concordantly or discordantly; of these: 7274230 mates make up the pairs; of these: 3194463 (43.91%) aligned 0 times 1535163 (21.10%) aligned exactly 1 time 2544604 (34.98%) aligned >1 times 93.77% overall alignment rate Time searching: 02:05:52 Overall time: 02:05:52 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] 6005952 / 21857074 = 0.2748 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 20:49:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978865/ERX3978865.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978865/ERX3978865.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978865/ERX3978865.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978865/ERX3978865.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 20:49:38: #1 read tag files... INFO @ Fri, 10 Dec 2021 20:49:38: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 20:49:45: 1000000 INFO @ Fri, 10 Dec 2021 20:49:52: 2000000 INFO @ Fri, 10 Dec 2021 20:49:59: 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 20:50:06: 4000000 INFO @ Fri, 10 Dec 2021 20:50:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978865/ERX3978865.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978865/ERX3978865.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978865/ERX3978865.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978865/ERX3978865.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 20:50:07: #1 read tag files... INFO @ Fri, 10 Dec 2021 20:50:07: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 20:50:13: 5000000 INFO @ Fri, 10 Dec 2021 20:50:14: 1000000 INFO @ Fri, 10 Dec 2021 20:50:21: 6000000 INFO @ Fri, 10 Dec 2021 20:50:21: 2000000 INFO @ Fri, 10 Dec 2021 20:50:28: 3000000 INFO @ Fri, 10 Dec 2021 20:50:29: 7000000 INFO @ Fri, 10 Dec 2021 20:50:35: 4000000 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 20:50:37: 8000000 INFO @ Fri, 10 Dec 2021 20:50:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978865/ERX3978865.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978865/ERX3978865.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978865/ERX3978865.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978865/ERX3978865.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 20:50:38: #1 read tag files... INFO @ Fri, 10 Dec 2021 20:50:38: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 20:50:42: 5000000 INFO @ Fri, 10 Dec 2021 20:50:44: 9000000 INFO @ Fri, 10 Dec 2021 20:50:45: 1000000 INFO @ Fri, 10 Dec 2021 20:50:48: 6000000 INFO @ Fri, 10 Dec 2021 20:50:52: 2000000 INFO @ Fri, 10 Dec 2021 20:50:52: 10000000 INFO @ Fri, 10 Dec 2021 20:50:55: 7000000 INFO @ Fri, 10 Dec 2021 20:50:59: 3000000 INFO @ Fri, 10 Dec 2021 20:51:00: 11000000 INFO @ Fri, 10 Dec 2021 20:51:03: 8000000 INFO @ Fri, 10 Dec 2021 20:51:06: 4000000 INFO @ Fri, 10 Dec 2021 20:51:08: 12000000 INFO @ Fri, 10 Dec 2021 20:51:10: 9000000 INFO @ Fri, 10 Dec 2021 20:51:13: 5000000 INFO @ Fri, 10 Dec 2021 20:51:15: 13000000 INFO @ Fri, 10 Dec 2021 20:51:17: 10000000 INFO @ Fri, 10 Dec 2021 20:51:20: 6000000 INFO @ Fri, 10 Dec 2021 20:51:23: 14000000 INFO @ Fri, 10 Dec 2021 20:51:24: 11000000 INFO @ Fri, 10 Dec 2021 20:51:27: 7000000 INFO @ Fri, 10 Dec 2021 20:51:31: 15000000 INFO @ Fri, 10 Dec 2021 20:51:31: 12000000 INFO @ Fri, 10 Dec 2021 20:51:34: 8000000 INFO @ Fri, 10 Dec 2021 20:51:38: 13000000 INFO @ Fri, 10 Dec 2021 20:51:39: 16000000 INFO @ Fri, 10 Dec 2021 20:51:41: 9000000 INFO @ Fri, 10 Dec 2021 20:51:45: 14000000 INFO @ Fri, 10 Dec 2021 20:51:47: 17000000 INFO @ Fri, 10 Dec 2021 20:51:48: 10000000 INFO @ Fri, 10 Dec 2021 20:51:52: 15000000 INFO @ Fri, 10 Dec 2021 20:51:54: 18000000 INFO @ Fri, 10 Dec 2021 20:51:55: 11000000 INFO @ Fri, 10 Dec 2021 20:51:59: 16000000 INFO @ Fri, 10 Dec 2021 20:52:02: 12000000 INFO @ Fri, 10 Dec 2021 20:52:02: 19000000 INFO @ Fri, 10 Dec 2021 20:52:06: 17000000 INFO @ Fri, 10 Dec 2021 20:52:09: 13000000 INFO @ Fri, 10 Dec 2021 20:52:10: 20000000 INFO @ Fri, 10 Dec 2021 20:52:13: 18000000 INFO @ Fri, 10 Dec 2021 20:52:16: 14000000 INFO @ Fri, 10 Dec 2021 20:52:17: 21000000 INFO @ Fri, 10 Dec 2021 20:52:20: 19000000 INFO @ Fri, 10 Dec 2021 20:52:23: 15000000 INFO @ Fri, 10 Dec 2021 20:52:25: 22000000 INFO @ Fri, 10 Dec 2021 20:52:27: 20000000 INFO @ Fri, 10 Dec 2021 20:52:30: 16000000 INFO @ Fri, 10 Dec 2021 20:52:32: 23000000 INFO @ Fri, 10 Dec 2021 20:52:34: 21000000 INFO @ Fri, 10 Dec 2021 20:52:37: 17000000 INFO @ Fri, 10 Dec 2021 20:52:40: 24000000 INFO @ Fri, 10 Dec 2021 20:52:41: 22000000 INFO @ Fri, 10 Dec 2021 20:52:44: 18000000 INFO @ Fri, 10 Dec 2021 20:52:48: 25000000 INFO @ Fri, 10 Dec 2021 20:52:48: 23000000 INFO @ Fri, 10 Dec 2021 20:52:51: 19000000 INFO @ Fri, 10 Dec 2021 20:52:55: 24000000 INFO @ Fri, 10 Dec 2021 20:52:55: 26000000 INFO @ Fri, 10 Dec 2021 20:52:58: 20000000 INFO @ Fri, 10 Dec 2021 20:53:02: 25000000 INFO @ Fri, 10 Dec 2021 20:53:03: 27000000 INFO @ Fri, 10 Dec 2021 20:53:05: 21000000 INFO @ Fri, 10 Dec 2021 20:53:09: 26000000 INFO @ Fri, 10 Dec 2021 20:53:11: 28000000 INFO @ Fri, 10 Dec 2021 20:53:12: 22000000 INFO @ Fri, 10 Dec 2021 20:53:17: 27000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 20:53:19: 29000000 INFO @ Fri, 10 Dec 2021 20:53:19: 23000000 INFO @ Fri, 10 Dec 2021 20:53:24: 28000000 INFO @ Fri, 10 Dec 2021 20:53:26: 24000000 INFO @ Fri, 10 Dec 2021 20:53:27: 30000000 INFO @ Fri, 10 Dec 2021 20:53:31: 29000000 INFO @ Fri, 10 Dec 2021 20:53:33: 25000000 INFO @ Fri, 10 Dec 2021 20:53:35: 31000000 INFO @ Fri, 10 Dec 2021 20:53:38: 30000000 INFO @ Fri, 10 Dec 2021 20:53:40: 26000000 INFO @ Fri, 10 Dec 2021 20:53:42: 32000000 INFO @ Fri, 10 Dec 2021 20:53:46: 31000000 INFO @ Fri, 10 Dec 2021 20:53:47: 27000000 INFO @ Fri, 10 Dec 2021 20:53:50: 33000000 INFO @ Fri, 10 Dec 2021 20:53:53: 32000000 INFO @ Fri, 10 Dec 2021 20:53:54: 28000000 INFO @ Fri, 10 Dec 2021 20:53:58: 34000000 INFO @ Fri, 10 Dec 2021 20:54:00: 33000000 INFO @ Fri, 10 Dec 2021 20:54:01: 29000000 INFO @ Fri, 10 Dec 2021 20:54:06: 35000000 INFO @ Fri, 10 Dec 2021 20:54:07: 34000000 INFO @ Fri, 10 Dec 2021 20:54:08: 30000000 INFO @ Fri, 10 Dec 2021 20:54:14: 36000000 INFO @ Fri, 10 Dec 2021 20:54:14: 35000000 INFO @ Fri, 10 Dec 2021 20:54:15: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 20:54:15: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 20:54:15: #1 total tags in treatment: 15682239 INFO @ Fri, 10 Dec 2021 20:54:15: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 20:54:15: #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 20:54:15: #1 tags after filtering in treatment: 14201819 INFO @ Fri, 10 Dec 2021 20:54:15: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 10 Dec 2021 20:54:15: #1 finished! INFO @ Fri, 10 Dec 2021 20:54:15: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 20:54:15: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 20:54:15: 31000000 INFO @ Fri, 10 Dec 2021 20:54:16: #2 number of paired peaks: 240 WARNING @ Fri, 10 Dec 2021 20:54:16: Fewer paired peaks (240) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 240 pairs to build model! INFO @ Fri, 10 Dec 2021 20:54:16: start model_add_line... INFO @ Fri, 10 Dec 2021 20:54:16: start X-correlation... INFO @ Fri, 10 Dec 2021 20:54:16: end of X-cor INFO @ Fri, 10 Dec 2021 20:54:16: #2 finished! INFO @ Fri, 10 Dec 2021 20:54:16: #2 predicted fragment length is 128 bps INFO @ Fri, 10 Dec 2021 20:54:16: #2 alternative fragment length(s) may be 128 bps INFO @ Fri, 10 Dec 2021 20:54:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978865/ERX3978865.05_model.r WARNING @ Fri, 10 Dec 2021 20:54:16: #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 20:54:16: #2 You may need to consider one of the other alternative d(s): 128 WARNING @ Fri, 10 Dec 2021 20:54:16: #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 20:54:16: #3 Call peaks... INFO @ Fri, 10 Dec 2021 20:54:16: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 20:54:21: 36000000 INFO @ Fri, 10 Dec 2021 20:54:22: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 20:54:22: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 20:54:22: #1 total tags in treatment: 15682239 INFO @ Fri, 10 Dec 2021 20:54:22: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 20:54:22: #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 20:54:22: 32000000 INFO @ Fri, 10 Dec 2021 20:54:22: #1 tags after filtering in treatment: 14201819 INFO @ Fri, 10 Dec 2021 20:54:22: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 10 Dec 2021 20:54:22: #1 finished! INFO @ Fri, 10 Dec 2021 20:54:22: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 20:54:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 20:54:23: #2 number of paired peaks: 240 WARNING @ Fri, 10 Dec 2021 20:54:23: Fewer paired peaks (240) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 240 pairs to build model! INFO @ Fri, 10 Dec 2021 20:54:23: start model_add_line... INFO @ Fri, 10 Dec 2021 20:54:23: start X-correlation... INFO @ Fri, 10 Dec 2021 20:54:23: end of X-cor INFO @ Fri, 10 Dec 2021 20:54:23: #2 finished! INFO @ Fri, 10 Dec 2021 20:54:23: #2 predicted fragment length is 128 bps INFO @ Fri, 10 Dec 2021 20:54:23: #2 alternative fragment length(s) may be 128 bps INFO @ Fri, 10 Dec 2021 20:54:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978865/ERX3978865.10_model.r WARNING @ Fri, 10 Dec 2021 20:54:23: #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 20:54:23: #2 You may need to consider one of the other alternative d(s): 128 WARNING @ Fri, 10 Dec 2021 20:54:23: #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 20:54:23: #3 Call peaks... INFO @ Fri, 10 Dec 2021 20:54:23: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 20:54:28: 33000000 INFO @ Fri, 10 Dec 2021 20:54:34: 34000000 INFO @ Fri, 10 Dec 2021 20:54:40: 35000000 INFO @ Fri, 10 Dec 2021 20:54:43: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 20:54:46: 36000000 INFO @ Fri, 10 Dec 2021 20:54:46: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 20:54:46: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 20:54:46: #1 total tags in treatment: 15682239 INFO @ Fri, 10 Dec 2021 20:54:46: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 20:54:46: #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 20:54:47: #1 tags after filtering in treatment: 14201819 INFO @ Fri, 10 Dec 2021 20:54:47: #1 Redundant rate of treatment: 0.09 INFO @ Fri, 10 Dec 2021 20:54:47: #1 finished! INFO @ Fri, 10 Dec 2021 20:54:47: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 20:54:47: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 20:54:48: #2 number of paired peaks: 240 WARNING @ Fri, 10 Dec 2021 20:54:48: Fewer paired peaks (240) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 240 pairs to build model! INFO @ Fri, 10 Dec 2021 20:54:48: start model_add_line... INFO @ Fri, 10 Dec 2021 20:54:48: start X-correlation... INFO @ Fri, 10 Dec 2021 20:54:48: end of X-cor INFO @ Fri, 10 Dec 2021 20:54:48: #2 finished! INFO @ Fri, 10 Dec 2021 20:54:48: #2 predicted fragment length is 128 bps INFO @ Fri, 10 Dec 2021 20:54:48: #2 alternative fragment length(s) may be 128 bps INFO @ Fri, 10 Dec 2021 20:54:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978865/ERX3978865.20_model.r WARNING @ Fri, 10 Dec 2021 20:54:48: #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 20:54:48: #2 You may need to consider one of the other alternative d(s): 128 WARNING @ Fri, 10 Dec 2021 20:54:48: #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 20:54:48: #3 Call peaks... INFO @ Fri, 10 Dec 2021 20:54:48: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 20:54:50: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 20:54:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978865/ERX3978865.05_peaks.xls INFO @ Fri, 10 Dec 2021 20:54:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978865/ERX3978865.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 20:54:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978865/ERX3978865.05_summits.bed INFO @ Fri, 10 Dec 2021 20:54:56: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5625 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 20:55:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978865/ERX3978865.10_peaks.xls INFO @ Fri, 10 Dec 2021 20:55:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978865/ERX3978865.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 20:55:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978865/ERX3978865.10_summits.bed INFO @ Fri, 10 Dec 2021 20:55:04: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2603 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 20:55:14: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 20:55:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978865/ERX3978865.20_peaks.xls INFO @ Fri, 10 Dec 2021 20:55:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978865/ERX3978865.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 20:55:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978865/ERX3978865.20_summits.bed INFO @ Fri, 10 Dec 2021 20:55:28: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (992 records, 4 fields): 3 millis CompletedMACS2peakCalling