Job ID = 14172103 SRX = SRX9103811 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 25983927 spots for SRR12621011/SRR12621011.sra Written 25983927 spots for SRR12621011/SRR12621011.sra fastq に変換しました。 bowtie でマッピング中... Your job 14172617 ("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: 00:24:02 25983927 reads; of these: 25983927 (100.00%) were paired; of these: 8217078 (31.62%) aligned concordantly 0 times 9342658 (35.96%) aligned concordantly exactly 1 time 8424191 (32.42%) aligned concordantly >1 times ---- 8217078 pairs aligned concordantly 0 times; of these: 1661206 (20.22%) aligned discordantly 1 time ---- 6555872 pairs aligned 0 times concordantly or discordantly; of these: 13111744 mates make up the pairs; of these: 10883173 (83.00%) aligned 0 times 626000 (4.77%) aligned exactly 1 time 1602571 (12.22%) aligned >1 times 79.06% overall alignment rate Time searching: 00:24:02 Overall time: 00:24:02 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] 6485303 / 19192710 = 0.3379 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 14:48:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9103811/SRX9103811.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9103811/SRX9103811.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9103811/SRX9103811.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9103811/SRX9103811.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 14:48:01: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:48:01: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:48:06: 1000000 INFO @ Sat, 11 Dec 2021 14:48:10: 2000000 INFO @ Sat, 11 Dec 2021 14:48:15: 3000000 INFO @ Sat, 11 Dec 2021 14:48:20: 4000000 INFO @ Sat, 11 Dec 2021 14:48:25: 5000000 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 14:48:30: 6000000 INFO @ Sat, 11 Dec 2021 14:48:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9103811/SRX9103811.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9103811/SRX9103811.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9103811/SRX9103811.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9103811/SRX9103811.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 14:48:31: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:48:31: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:48:35: 7000000 INFO @ Sat, 11 Dec 2021 14:48:36: 1000000 INFO @ Sat, 11 Dec 2021 14:48:41: 8000000 INFO @ Sat, 11 Dec 2021 14:48:41: 2000000 INFO @ Sat, 11 Dec 2021 14:48:46: 9000000 INFO @ Sat, 11 Dec 2021 14:48:47: 3000000 INFO @ Sat, 11 Dec 2021 14:48:51: 10000000 INFO @ Sat, 11 Dec 2021 14:48:52: 4000000 INFO @ Sat, 11 Dec 2021 14:48:57: 11000000 INFO @ Sat, 11 Dec 2021 14:48:57: 5000000 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 14:49:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9103811/SRX9103811.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9103811/SRX9103811.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9103811/SRX9103811.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9103811/SRX9103811.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 14:49:01: #1 read tag files... INFO @ Sat, 11 Dec 2021 14:49:01: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 14:49:02: 12000000 INFO @ Sat, 11 Dec 2021 14:49:03: 6000000 INFO @ Sat, 11 Dec 2021 14:49:07: 1000000 INFO @ Sat, 11 Dec 2021 14:49:08: 13000000 INFO @ Sat, 11 Dec 2021 14:49:09: 7000000 INFO @ Sat, 11 Dec 2021 14:49:13: 2000000 INFO @ Sat, 11 Dec 2021 14:49:14: 14000000 INFO @ Sat, 11 Dec 2021 14:49:14: 8000000 INFO @ Sat, 11 Dec 2021 14:49:19: 15000000 INFO @ Sat, 11 Dec 2021 14:49:20: 3000000 INFO @ Sat, 11 Dec 2021 14:49:20: 9000000 INFO @ Sat, 11 Dec 2021 14:49:25: 16000000 INFO @ Sat, 11 Dec 2021 14:49:26: 10000000 INFO @ Sat, 11 Dec 2021 14:49:26: 4000000 INFO @ Sat, 11 Dec 2021 14:49:31: 17000000 INFO @ Sat, 11 Dec 2021 14:49:32: 11000000 INFO @ Sat, 11 Dec 2021 14:49:33: 5000000 INFO @ Sat, 11 Dec 2021 14:49:36: 18000000 INFO @ Sat, 11 Dec 2021 14:49:37: 12000000 INFO @ Sat, 11 Dec 2021 14:49:39: 6000000 INFO @ Sat, 11 Dec 2021 14:49:42: 19000000 INFO @ Sat, 11 Dec 2021 14:49:43: 13000000 INFO @ Sat, 11 Dec 2021 14:49:46: 7000000 INFO @ Sat, 11 Dec 2021 14:49:47: 20000000 INFO @ Sat, 11 Dec 2021 14:49:49: 14000000 INFO @ Sat, 11 Dec 2021 14:49:52: 8000000 INFO @ Sat, 11 Dec 2021 14:49:53: 21000000 INFO @ Sat, 11 Dec 2021 14:49:54: 15000000 INFO @ Sat, 11 Dec 2021 14:49:59: 22000000 INFO @ Sat, 11 Dec 2021 14:49:59: 9000000 INFO @ Sat, 11 Dec 2021 14:50:00: 16000000 INFO @ Sat, 11 Dec 2021 14:50:04: 23000000 INFO @ Sat, 11 Dec 2021 14:50:05: 10000000 INFO @ Sat, 11 Dec 2021 14:50:06: 17000000 INFO @ Sat, 11 Dec 2021 14:50:10: 24000000 INFO @ Sat, 11 Dec 2021 14:50:11: 18000000 INFO @ Sat, 11 Dec 2021 14:50:12: 11000000 INFO @ Sat, 11 Dec 2021 14:50:16: 25000000 INFO @ Sat, 11 Dec 2021 14:50:17: 19000000 INFO @ Sat, 11 Dec 2021 14:50:18: 12000000 INFO @ Sat, 11 Dec 2021 14:50:22: 26000000 INFO @ Sat, 11 Dec 2021 14:50:23: 20000000 INFO @ Sat, 11 Dec 2021 14:50:25: 13000000 INFO @ Sat, 11 Dec 2021 14:50:27: 27000000 INFO @ Sat, 11 Dec 2021 14:50:28: 21000000 INFO @ Sat, 11 Dec 2021 14:50:31: 14000000 INFO @ Sat, 11 Dec 2021 14:50:33: 28000000 INFO @ Sat, 11 Dec 2021 14:50:34: 22000000 INFO @ Sat, 11 Dec 2021 14:50:34: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 14:50:34: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 14:50:34: #1 total tags in treatment: 11451415 INFO @ Sat, 11 Dec 2021 14:50:34: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:50:34: #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 14:50:34: #1 tags after filtering in treatment: 8725056 INFO @ Sat, 11 Dec 2021 14:50:34: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 11 Dec 2021 14:50:34: #1 finished! INFO @ Sat, 11 Dec 2021 14:50:34: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:50:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:50:35: #2 number of paired peaks: 941 WARNING @ Sat, 11 Dec 2021 14:50:35: Fewer paired peaks (941) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 941 pairs to build model! INFO @ Sat, 11 Dec 2021 14:50:35: start model_add_line... INFO @ Sat, 11 Dec 2021 14:50:35: start X-correlation... INFO @ Sat, 11 Dec 2021 14:50:35: end of X-cor INFO @ Sat, 11 Dec 2021 14:50:35: #2 finished! INFO @ Sat, 11 Dec 2021 14:50:35: #2 predicted fragment length is 67 bps INFO @ Sat, 11 Dec 2021 14:50:35: #2 alternative fragment length(s) may be 67 bps INFO @ Sat, 11 Dec 2021 14:50:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9103811/SRX9103811.05_model.r WARNING @ Sat, 11 Dec 2021 14:50:35: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:50:35: #2 You may need to consider one of the other alternative d(s): 67 WARNING @ Sat, 11 Dec 2021 14:50:35: #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 14:50:35: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:50:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:50:38: 15000000 INFO @ Sat, 11 Dec 2021 14:50:39: 23000000 INFO @ Sat, 11 Dec 2021 14:50:44: 16000000 INFO @ Sat, 11 Dec 2021 14:50:45: 24000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 14:50:50: 25000000 INFO @ Sat, 11 Dec 2021 14:50:51: 17000000 INFO @ Sat, 11 Dec 2021 14:50:52: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:50:56: 26000000 INFO @ Sat, 11 Dec 2021 14:50:57: 18000000 INFO @ Sat, 11 Dec 2021 14:51:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9103811/SRX9103811.05_peaks.xls INFO @ Sat, 11 Dec 2021 14:51:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9103811/SRX9103811.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:51:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9103811/SRX9103811.05_summits.bed INFO @ Sat, 11 Dec 2021 14:51:01: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (9138 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 14:51:02: 27000000 INFO @ Sat, 11 Dec 2021 14:51:04: 19000000 INFO @ Sat, 11 Dec 2021 14:51:07: 28000000 INFO @ Sat, 11 Dec 2021 14:51:08: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 14:51:08: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 14:51:08: #1 total tags in treatment: 11451415 INFO @ Sat, 11 Dec 2021 14:51:08: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:51:08: #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 14:51:08: #1 tags after filtering in treatment: 8725056 INFO @ Sat, 11 Dec 2021 14:51:08: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 11 Dec 2021 14:51:08: #1 finished! INFO @ Sat, 11 Dec 2021 14:51:08: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:51:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:51:09: #2 number of paired peaks: 941 WARNING @ Sat, 11 Dec 2021 14:51:09: Fewer paired peaks (941) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 941 pairs to build model! INFO @ Sat, 11 Dec 2021 14:51:09: start model_add_line... INFO @ Sat, 11 Dec 2021 14:51:09: start X-correlation... INFO @ Sat, 11 Dec 2021 14:51:09: end of X-cor INFO @ Sat, 11 Dec 2021 14:51:09: #2 finished! INFO @ Sat, 11 Dec 2021 14:51:09: #2 predicted fragment length is 67 bps INFO @ Sat, 11 Dec 2021 14:51:09: #2 alternative fragment length(s) may be 67 bps INFO @ Sat, 11 Dec 2021 14:51:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9103811/SRX9103811.10_model.r WARNING @ Sat, 11 Dec 2021 14:51:09: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:51:09: #2 You may need to consider one of the other alternative d(s): 67 WARNING @ Sat, 11 Dec 2021 14:51:09: #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 14:51:09: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:51:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:51:10: 20000000 INFO @ Sat, 11 Dec 2021 14:51:16: 21000000 INFO @ Sat, 11 Dec 2021 14:51:22: 22000000 INFO @ Sat, 11 Dec 2021 14:51:26: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:51:28: 23000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 14:51:35: 24000000 INFO @ Sat, 11 Dec 2021 14:51:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9103811/SRX9103811.10_peaks.xls INFO @ Sat, 11 Dec 2021 14:51:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9103811/SRX9103811.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:51:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9103811/SRX9103811.10_summits.bed INFO @ Sat, 11 Dec 2021 14:51:35: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4149 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 14:51:41: 25000000 INFO @ Sat, 11 Dec 2021 14:51:47: 26000000 INFO @ Sat, 11 Dec 2021 14:51:53: 27000000 INFO @ Sat, 11 Dec 2021 14:51:59: 28000000 INFO @ Sat, 11 Dec 2021 14:51:59: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 14:51:59: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 14:51:59: #1 total tags in treatment: 11451415 INFO @ Sat, 11 Dec 2021 14:51:59: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 14:51:59: #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 14:52:00: #1 tags after filtering in treatment: 8725056 INFO @ Sat, 11 Dec 2021 14:52:00: #1 Redundant rate of treatment: 0.24 INFO @ Sat, 11 Dec 2021 14:52:00: #1 finished! INFO @ Sat, 11 Dec 2021 14:52:00: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 14:52:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 14:52:00: #2 number of paired peaks: 941 WARNING @ Sat, 11 Dec 2021 14:52:00: Fewer paired peaks (941) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 941 pairs to build model! INFO @ Sat, 11 Dec 2021 14:52:00: start model_add_line... INFO @ Sat, 11 Dec 2021 14:52:00: start X-correlation... INFO @ Sat, 11 Dec 2021 14:52:00: end of X-cor INFO @ Sat, 11 Dec 2021 14:52:00: #2 finished! INFO @ Sat, 11 Dec 2021 14:52:00: #2 predicted fragment length is 67 bps INFO @ Sat, 11 Dec 2021 14:52:00: #2 alternative fragment length(s) may be 67 bps INFO @ Sat, 11 Dec 2021 14:52:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9103811/SRX9103811.20_model.r WARNING @ Sat, 11 Dec 2021 14:52:00: #2 Since the d (67) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 14:52:00: #2 You may need to consider one of the other alternative d(s): 67 WARNING @ Sat, 11 Dec 2021 14:52:00: #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 14:52:00: #3 Call peaks... INFO @ Sat, 11 Dec 2021 14:52:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 14:52:18: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 14:52:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9103811/SRX9103811.20_peaks.xls INFO @ Sat, 11 Dec 2021 14:52:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9103811/SRX9103811.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 14:52:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9103811/SRX9103811.20_summits.bed INFO @ Sat, 11 Dec 2021 14:52:27: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (683 records, 4 fields): 4 millis CompletedMACS2peakCalling