Job ID = 14168187 SRX = ERX3978835 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 30555247 spots for ERR3975904/ERR3975904.sra Written 30555247 spots for ERR3975904/ERR3975904.sra fastq に変換しました。 bowtie でマッピング中... Your job 14169535 ("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: 02:10:42 30555247 reads; of these: 30555247 (100.00%) were paired; of these: 10315934 (33.76%) aligned concordantly 0 times 16557058 (54.19%) aligned concordantly exactly 1 time 3682255 (12.05%) aligned concordantly >1 times ---- 10315934 pairs aligned concordantly 0 times; of these: 1127686 (10.93%) aligned discordantly 1 time ---- 9188248 pairs aligned 0 times concordantly or discordantly; of these: 18376496 mates make up the pairs; of these: 9204052 (50.09%) aligned 0 times 5783441 (31.47%) aligned exactly 1 time 3389003 (18.44%) aligned >1 times 84.94% overall alignment rate Time searching: 02:10:42 Overall time: 02:10:42 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] 16369381 / 20988116 = 0.7799 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 18:29:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978835/ERX3978835.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978835/ERX3978835.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978835/ERX3978835.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978835/ERX3978835.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 18:29:44: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:29:44: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:29:51: 1000000 INFO @ Fri, 10 Dec 2021 18:29:57: 2000000 INFO @ Fri, 10 Dec 2021 18:30:03: 3000000 INFO @ Fri, 10 Dec 2021 18:30:09: 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 18:30:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978835/ERX3978835.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978835/ERX3978835.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978835/ERX3978835.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978835/ERX3978835.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 18:30:13: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:30:13: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:30:15: 5000000 INFO @ Fri, 10 Dec 2021 18:30:19: 1000000 INFO @ Fri, 10 Dec 2021 18:30:21: 6000000 INFO @ Fri, 10 Dec 2021 18:30:25: 2000000 INFO @ Fri, 10 Dec 2021 18:30:28: 7000000 INFO @ Fri, 10 Dec 2021 18:30:32: 3000000 INFO @ Fri, 10 Dec 2021 18:30:34: 8000000 INFO @ Fri, 10 Dec 2021 18:30:38: 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 18:30:42: 9000000 INFO @ Fri, 10 Dec 2021 18:30:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978835/ERX3978835.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978835/ERX3978835.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978835/ERX3978835.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978835/ERX3978835.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 18:30:43: #1 read tag files... INFO @ Fri, 10 Dec 2021 18:30:43: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 18:30:44: 5000000 INFO @ Fri, 10 Dec 2021 18:30:48: 10000000 INFO @ Fri, 10 Dec 2021 18:30:51: 6000000 INFO @ Fri, 10 Dec 2021 18:30:52: 1000000 INFO @ Fri, 10 Dec 2021 18:30:55: 11000000 INFO @ Fri, 10 Dec 2021 18:30:58: 7000000 INFO @ Fri, 10 Dec 2021 18:31:00: 2000000 INFO @ Fri, 10 Dec 2021 18:31:02: 12000000 INFO @ Fri, 10 Dec 2021 18:31:05: 8000000 INFO @ Fri, 10 Dec 2021 18:31:07: 3000000 INFO @ Fri, 10 Dec 2021 18:31:08: 13000000 INFO @ Fri, 10 Dec 2021 18:31:12: 9000000 INFO @ Fri, 10 Dec 2021 18:31:14: 4000000 INFO @ Fri, 10 Dec 2021 18:31:15: 14000000 INFO @ Fri, 10 Dec 2021 18:31:19: 10000000 INFO @ Fri, 10 Dec 2021 18:31:21: 5000000 INFO @ Fri, 10 Dec 2021 18:31:22: 15000000 INFO @ Fri, 10 Dec 2021 18:31:25: 11000000 INFO @ Fri, 10 Dec 2021 18:31:28: 6000000 INFO @ Fri, 10 Dec 2021 18:31:29: 16000000 INFO @ Fri, 10 Dec 2021 18:31:33: 12000000 INFO @ Fri, 10 Dec 2021 18:31:36: 17000000 INFO @ Fri, 10 Dec 2021 18:31:36: 7000000 INFO @ Fri, 10 Dec 2021 18:31:40: 13000000 INFO @ Fri, 10 Dec 2021 18:31:42: 18000000 INFO @ Fri, 10 Dec 2021 18:31:43: 8000000 INFO @ Fri, 10 Dec 2021 18:31:48: 14000000 INFO @ Fri, 10 Dec 2021 18:31:49: 19000000 INFO @ Fri, 10 Dec 2021 18:31:50: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 18:31:50: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 18:31:50: #1 total tags in treatment: 4517741 INFO @ Fri, 10 Dec 2021 18:31:50: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:31:50: #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 18:31:50: #1 tags after filtering in treatment: 4165413 INFO @ Fri, 10 Dec 2021 18:31:50: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 10 Dec 2021 18:31:50: #1 finished! INFO @ Fri, 10 Dec 2021 18:31:50: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:31:50: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:31:50: #2 number of paired peaks: 758 WARNING @ Fri, 10 Dec 2021 18:31:50: Fewer paired peaks (758) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 758 pairs to build model! INFO @ Fri, 10 Dec 2021 18:31:50: start model_add_line... INFO @ Fri, 10 Dec 2021 18:31:50: start X-correlation... INFO @ Fri, 10 Dec 2021 18:31:50: 9000000 INFO @ Fri, 10 Dec 2021 18:31:50: end of X-cor INFO @ Fri, 10 Dec 2021 18:31:50: #2 finished! INFO @ Fri, 10 Dec 2021 18:31:50: #2 predicted fragment length is 132 bps INFO @ Fri, 10 Dec 2021 18:31:50: #2 alternative fragment length(s) may be 132 bps INFO @ Fri, 10 Dec 2021 18:31:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978835/ERX3978835.05_model.r WARNING @ Fri, 10 Dec 2021 18:31:50: #2 Since the d (132) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 18:31:50: #2 You may need to consider one of the other alternative d(s): 132 WARNING @ Fri, 10 Dec 2021 18:31:50: #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 18:31:50: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:31:50: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 18:31:56: 15000000 INFO @ Fri, 10 Dec 2021 18:31:57: 10000000 INFO @ Fri, 10 Dec 2021 18:31:59: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:32:03: 16000000 INFO @ Fri, 10 Dec 2021 18:32:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978835/ERX3978835.05_peaks.xls INFO @ Fri, 10 Dec 2021 18:32:04: 11000000 INFO @ Fri, 10 Dec 2021 18:32:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978835/ERX3978835.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:32:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978835/ERX3978835.05_summits.bed INFO @ Fri, 10 Dec 2021 18:32:04: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3635 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 18:32:11: 17000000 INFO @ Fri, 10 Dec 2021 18:32:11: 12000000 INFO @ Fri, 10 Dec 2021 18:32:18: 18000000 INFO @ Fri, 10 Dec 2021 18:32:19: 13000000 INFO @ Fri, 10 Dec 2021 18:32:25: 19000000 INFO @ Fri, 10 Dec 2021 18:32:26: 14000000 INFO @ Fri, 10 Dec 2021 18:32:26: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 18:32:26: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 18:32:26: #1 total tags in treatment: 4517741 INFO @ Fri, 10 Dec 2021 18:32:26: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:32:26: #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 18:32:26: #1 tags after filtering in treatment: 4165413 INFO @ Fri, 10 Dec 2021 18:32:26: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 10 Dec 2021 18:32:26: #1 finished! INFO @ Fri, 10 Dec 2021 18:32:26: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:32:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:32:26: #2 number of paired peaks: 758 WARNING @ Fri, 10 Dec 2021 18:32:26: Fewer paired peaks (758) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 758 pairs to build model! INFO @ Fri, 10 Dec 2021 18:32:26: start model_add_line... INFO @ Fri, 10 Dec 2021 18:32:26: start X-correlation... INFO @ Fri, 10 Dec 2021 18:32:26: end of X-cor INFO @ Fri, 10 Dec 2021 18:32:26: #2 finished! INFO @ Fri, 10 Dec 2021 18:32:26: #2 predicted fragment length is 132 bps INFO @ Fri, 10 Dec 2021 18:32:26: #2 alternative fragment length(s) may be 132 bps INFO @ Fri, 10 Dec 2021 18:32:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978835/ERX3978835.10_model.r WARNING @ Fri, 10 Dec 2021 18:32:26: #2 Since the d (132) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 18:32:26: #2 You may need to consider one of the other alternative d(s): 132 WARNING @ Fri, 10 Dec 2021 18:32:26: #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 18:32:26: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:32:26: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 18:32:33: 15000000 INFO @ Fri, 10 Dec 2021 18:32:35: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:32:39: 16000000 INFO @ Fri, 10 Dec 2021 18:32:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978835/ERX3978835.10_peaks.xls INFO @ Fri, 10 Dec 2021 18:32:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978835/ERX3978835.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:32:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978835/ERX3978835.10_summits.bed INFO @ Fri, 10 Dec 2021 18:32:41: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1276 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 18:32:46: 17000000 INFO @ Fri, 10 Dec 2021 18:32:52: 18000000 INFO @ Fri, 10 Dec 2021 18:32:58: 19000000 INFO @ Fri, 10 Dec 2021 18:32:59: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 18:32:59: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 18:32:59: #1 total tags in treatment: 4517741 INFO @ Fri, 10 Dec 2021 18:32:59: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 18:32:59: #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 18:32:59: #1 tags after filtering in treatment: 4165413 INFO @ Fri, 10 Dec 2021 18:32:59: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 10 Dec 2021 18:32:59: #1 finished! INFO @ Fri, 10 Dec 2021 18:32:59: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 18:32:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 18:33:00: #2 number of paired peaks: 758 WARNING @ Fri, 10 Dec 2021 18:33:00: Fewer paired peaks (758) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 758 pairs to build model! INFO @ Fri, 10 Dec 2021 18:33:00: start model_add_line... INFO @ Fri, 10 Dec 2021 18:33:00: start X-correlation... INFO @ Fri, 10 Dec 2021 18:33:00: end of X-cor INFO @ Fri, 10 Dec 2021 18:33:00: #2 finished! INFO @ Fri, 10 Dec 2021 18:33:00: #2 predicted fragment length is 132 bps INFO @ Fri, 10 Dec 2021 18:33:00: #2 alternative fragment length(s) may be 132 bps INFO @ Fri, 10 Dec 2021 18:33:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978835/ERX3978835.20_model.r WARNING @ Fri, 10 Dec 2021 18:33:00: #2 Since the d (132) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 18:33:00: #2 You may need to consider one of the other alternative d(s): 132 WARNING @ Fri, 10 Dec 2021 18:33:00: #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 18:33:00: #3 Call peaks... INFO @ Fri, 10 Dec 2021 18:33:00: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 18:33:08: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 18:33:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978835/ERX3978835.20_peaks.xls INFO @ Fri, 10 Dec 2021 18:33:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978835/ERX3978835.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 18:33:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978835/ERX3978835.20_summits.bed INFO @ Fri, 10 Dec 2021 18:33:14: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (497 records, 4 fields): 3 millis CompletedMACS2peakCalling