Job ID = 14168327 SRX = ERX3978737 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 29810279 spots for ERR3975746/ERR3975746.sra Written 29810279 spots for ERR3975746/ERR3975746.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169596 ("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: 01:07:27 29810279 reads; of these: 29810279 (100.00%) were paired; of these: 11461695 (38.45%) aligned concordantly 0 times 9308232 (31.22%) aligned concordantly exactly 1 time 9040352 (30.33%) aligned concordantly >1 times ---- 11461695 pairs aligned concordantly 0 times; of these: 3183339 (27.77%) aligned discordantly 1 time ---- 8278356 pairs aligned 0 times concordantly or discordantly; of these: 16556712 mates make up the pairs; of these: 11234685 (67.86%) aligned 0 times 557586 (3.37%) aligned exactly 1 time 4764441 (28.78%) aligned >1 times 81.16% overall alignment rate Time searching: 01:07:27 Overall time: 01:07:27 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 32 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] 8070240 / 21404255 = 0.3770 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 18:50:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978737/ERX3978737.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978737/ERX3978737.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978737/ERX3978737.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978737/ERX3978737.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 18:50:20: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:50:20: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:50:27: 1000000 INFO @ Fri, 10 Dec 2021 18:50:34: 2000000 INFO @ Fri, 10 Dec 2021 18:50:42: 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 18:50:49: 4000000 INFO @ Fri, 10 Dec 2021 18:50:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978737/ERX3978737.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978737/ERX3978737.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978737/ERX3978737.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978737/ERX3978737.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 18:50:50: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:50:50: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:50:57: 5000000 INFO @ Fri, 10 Dec 2021 18:50:59: 1000000 INFO @ Fri, 10 Dec 2021 18:51:06: 6000000 INFO @ Fri, 10 Dec 2021 18:51:08: 2000000 INFO @ Fri, 10 Dec 2021 18:51:14: 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 18:51:18: 3000000 INFO @ Fri, 10 Dec 2021 18:51:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978737/ERX3978737.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978737/ERX3978737.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978737/ERX3978737.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978737/ERX3978737.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 18:51:20: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:51:20: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:51:23: 8000000 INFO @ Fri, 10 Dec 2021 18:51:28: 4000000 INFO @ Fri, 10 Dec 2021 18:51:28: 1000000 INFO @ Fri, 10 Dec 2021 18:51:31: 9000000 INFO @ Fri, 10 Dec 2021 18:51:37: 2000000 INFO @ Fri, 10 Dec 2021 18:51:38: 5000000 INFO @ Fri, 10 Dec 2021 18:51:40: 10000000 INFO @ Fri, 10 Dec 2021 18:51:45: 3000000 INFO @ Fri, 10 Dec 2021 18:51:47: 6000000 INFO @ Fri, 10 Dec 2021 18:51:48: 11000000 INFO @ Fri, 10 Dec 2021 18:51:54: 4000000 INFO @ Fri, 10 Dec 2021 18:51:57: 12000000 INFO @ Fri, 10 Dec 2021 18:51:57: 7000000 INFO @ Fri, 10 Dec 2021 18:52:02: 5000000 INFO @ Fri, 10 Dec 2021 18:52:05: 13000000 INFO @ Fri, 10 Dec 2021 18:52:07: 8000000 INFO @ Fri, 10 Dec 2021 18:52:11: 6000000 INFO @ Fri, 10 Dec 2021 18:52:14: 14000000 INFO @ Fri, 10 Dec 2021 18:52:16: 9000000 INFO @ Fri, 10 Dec 2021 18:52:20: 7000000 INFO @ Fri, 10 Dec 2021 18:52:22: 15000000 INFO @ Fri, 10 Dec 2021 18:52:26: 10000000 INFO @ Fri, 10 Dec 2021 18:52:28: 8000000 INFO @ Fri, 10 Dec 2021 18:52:31: 16000000 INFO @ Fri, 10 Dec 2021 18:52:36: 11000000 INFO @ Fri, 10 Dec 2021 18:52:37: 9000000 INFO @ Fri, 10 Dec 2021 18:52:40: 17000000 INFO @ Fri, 10 Dec 2021 18:52:45: 12000000 INFO @ Fri, 10 Dec 2021 18:52:46: 10000000 INFO @ Fri, 10 Dec 2021 18:52:48: 18000000 INFO @ Fri, 10 Dec 2021 18:52:54: 11000000 INFO @ Fri, 10 Dec 2021 18:52:55: 13000000 INFO @ Fri, 10 Dec 2021 18:52:57: 19000000 INFO @ Fri, 10 Dec 2021 18:53:03: 12000000 INFO @ Fri, 10 Dec 2021 18:53:04: 14000000 INFO @ Fri, 10 Dec 2021 18:53:05: 20000000 INFO @ Fri, 10 Dec 2021 18:53:11: 13000000 INFO @ Fri, 10 Dec 2021 18:53:13: 21000000 INFO @ Fri, 10 Dec 2021 18:53:14: 15000000 INFO @ Fri, 10 Dec 2021 18:53:20: 14000000 INFO @ Fri, 10 Dec 2021 18:53:22: 22000000 INFO @ Fri, 10 Dec 2021 18:53:23: 16000000 INFO @ Fri, 10 Dec 2021 18:53:28: 15000000 INFO @ Fri, 10 Dec 2021 18:53:30: 23000000 INFO @ Fri, 10 Dec 2021 18:53:33: 17000000 INFO @ Fri, 10 Dec 2021 18:53:37: 16000000 INFO @ Fri, 10 Dec 2021 18:53:38: 24000000 INFO @ Fri, 10 Dec 2021 18:53:42: 18000000 INFO @ Fri, 10 Dec 2021 18:53:45: 17000000 INFO @ Fri, 10 Dec 2021 18:53:46: 25000000 INFO @ Fri, 10 Dec 2021 18:53:52: 19000000 INFO @ Fri, 10 Dec 2021 18:53:54: 18000000 INFO @ Fri, 10 Dec 2021 18:53:54: 26000000 INFO @ Fri, 10 Dec 2021 18:54:01: 20000000 INFO @ Fri, 10 Dec 2021 18:54:02: 19000000 INFO @ Fri, 10 Dec 2021 18:54:03: 27000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 18:54:10: 20000000 INFO @ Fri, 10 Dec 2021 18:54:11: 21000000 INFO @ Fri, 10 Dec 2021 18:54:11: 28000000 INFO @ Fri, 10 Dec 2021 18:54:18: 21000000 INFO @ Fri, 10 Dec 2021 18:54:19: 29000000 INFO @ Fri, 10 Dec 2021 18:54:20: 22000000 INFO @ Fri, 10 Dec 2021 18:54:26: 22000000 INFO @ Fri, 10 Dec 2021 18:54:28: 30000000 INFO @ Fri, 10 Dec 2021 18:54:29: 23000000 INFO @ Fri, 10 Dec 2021 18:54:34: 23000000 INFO @ Fri, 10 Dec 2021 18:54:36: 31000000 INFO @ Fri, 10 Dec 2021 18:54:38: 24000000 INFO @ Fri, 10 Dec 2021 18:54:42: 24000000 INFO @ Fri, 10 Dec 2021 18:54:44: 32000000 INFO @ Fri, 10 Dec 2021 18:54:47: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 18:54:47: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 18:54:47: #1 total tags in treatment: 10617234 INFO @ Fri, 10 Dec 2021 18:54:47: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:54:47: #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 18:54:47: #1 tags after filtering in treatment: 7625934 INFO @ Fri, 10 Dec 2021 18:54:47: #1 Redundant rate of treatment: 0.28 INFO @ Fri, 10 Dec 2021 18:54:47: #1 finished! INFO @ Fri, 10 Dec 2021 18:54:47: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:54:47: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:54:48: #2 number of paired peaks: 2545 INFO @ Fri, 10 Dec 2021 18:54:48: start model_add_line... INFO @ Fri, 10 Dec 2021 18:54:48: 25000000 INFO @ Fri, 10 Dec 2021 18:54:48: start X-correlation... INFO @ Fri, 10 Dec 2021 18:54:48: end of X-cor INFO @ Fri, 10 Dec 2021 18:54:48: #2 finished! INFO @ Fri, 10 Dec 2021 18:54:48: #2 predicted fragment length is 209 bps INFO @ Fri, 10 Dec 2021 18:54:48: #2 alternative fragment length(s) may be 209 bps INFO @ Fri, 10 Dec 2021 18:54:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978737/ERX3978737.05_model.r WARNING @ Fri, 10 Dec 2021 18:54:48: #2 Since the d (209) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 18:54:48: #2 You may need to consider one of the other alternative d(s): 209 WARNING @ Fri, 10 Dec 2021 18:54:48: #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 18:54:48: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:54:48: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 18:54:50: 25000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 18:54:57: 26000000 INFO @ Fri, 10 Dec 2021 18:54:58: 26000000 INFO @ Fri, 10 Dec 2021 18:55:07: 27000000 INFO @ Fri, 10 Dec 2021 18:55:07: 27000000 INFO @ Fri, 10 Dec 2021 18:55:08: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:55:17: 28000000 INFO @ Fri, 10 Dec 2021 18:55:17: 28000000 INFO @ Fri, 10 Dec 2021 18:55:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978737/ERX3978737.05_peaks.xls INFO @ Fri, 10 Dec 2021 18:55:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978737/ERX3978737.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:55:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978737/ERX3978737.05_summits.bed INFO @ Fri, 10 Dec 2021 18:55:19: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (11904 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 18:55:27: 29000000 INFO @ Fri, 10 Dec 2021 18:55:27: 29000000 INFO @ Fri, 10 Dec 2021 18:55:37: 30000000 INFO @ Fri, 10 Dec 2021 18:55:38: 30000000 INFO @ Fri, 10 Dec 2021 18:55:47: 31000000 INFO @ Fri, 10 Dec 2021 18:55:48: 31000000 INFO @ Fri, 10 Dec 2021 18:55:57: 32000000 INFO @ Fri, 10 Dec 2021 18:55:58: 32000000 INFO @ Fri, 10 Dec 2021 18:56:00: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 18:56:00: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 18:56:00: #1 total tags in treatment: 10617234 INFO @ Fri, 10 Dec 2021 18:56:00: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:56:00: #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 18:56:00: #1 tags after filtering in treatment: 7625934 INFO @ Fri, 10 Dec 2021 18:56:00: #1 Redundant rate of treatment: 0.28 INFO @ Fri, 10 Dec 2021 18:56:00: #1 finished! INFO @ Fri, 10 Dec 2021 18:56:00: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:56:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:56:00: #1 tag size is determined as 125 bps INFO @ Fri, 10 Dec 2021 18:56:00: #1 tag size = 125 INFO @ Fri, 10 Dec 2021 18:56:00: #1 total tags in treatment: 10617234 INFO @ Fri, 10 Dec 2021 18:56:00: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:56:00: #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 18:56:01: #1 tags after filtering in treatment: 7625934 INFO @ Fri, 10 Dec 2021 18:56:01: #1 Redundant rate of treatment: 0.28 INFO @ Fri, 10 Dec 2021 18:56:01: #1 finished! INFO @ Fri, 10 Dec 2021 18:56:01: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:56:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:56:01: #2 number of paired peaks: 2545 INFO @ Fri, 10 Dec 2021 18:56:01: start model_add_line... INFO @ Fri, 10 Dec 2021 18:56:01: start X-correlation... INFO @ Fri, 10 Dec 2021 18:56:01: end of X-cor INFO @ Fri, 10 Dec 2021 18:56:01: #2 finished! INFO @ Fri, 10 Dec 2021 18:56:01: #2 predicted fragment length is 209 bps INFO @ Fri, 10 Dec 2021 18:56:01: #2 alternative fragment length(s) may be 209 bps INFO @ Fri, 10 Dec 2021 18:56:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978737/ERX3978737.10_model.r WARNING @ Fri, 10 Dec 2021 18:56:01: #2 Since the d (209) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 18:56:01: #2 You may need to consider one of the other alternative d(s): 209 WARNING @ Fri, 10 Dec 2021 18:56:01: #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 18:56:01: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:56:01: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 18:56:01: #2 number of paired peaks: 2545 INFO @ Fri, 10 Dec 2021 18:56:01: start model_add_line... INFO @ Fri, 10 Dec 2021 18:56:01: start X-correlation... INFO @ Fri, 10 Dec 2021 18:56:01: end of X-cor INFO @ Fri, 10 Dec 2021 18:56:01: #2 finished! INFO @ Fri, 10 Dec 2021 18:56:01: #2 predicted fragment length is 209 bps INFO @ Fri, 10 Dec 2021 18:56:01: #2 alternative fragment length(s) may be 209 bps INFO @ Fri, 10 Dec 2021 18:56:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978737/ERX3978737.20_model.r WARNING @ Fri, 10 Dec 2021 18:56:01: #2 Since the d (209) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 18:56:01: #2 You may need to consider one of the other alternative d(s): 209 WARNING @ Fri, 10 Dec 2021 18:56:01: #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 18:56:01: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:56:01: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 18:56:21: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:56:22: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:56:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978737/ERX3978737.20_peaks.xls INFO @ Fri, 10 Dec 2021 18:56:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978737/ERX3978737.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:56:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978737/ERX3978737.20_summits.bed INFO @ Fri, 10 Dec 2021 18:56:32: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2927 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 18:56:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978737/ERX3978737.10_peaks.xls INFO @ Fri, 10 Dec 2021 18:56:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978737/ERX3978737.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:56:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978737/ERX3978737.10_summits.bed INFO @ Fri, 10 Dec 2021 18:56:33: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (7520 records, 4 fields): 9 millis CompletedMACS2peakCalling