Job ID = 14168876 SRX = ERX3978897 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 21521182 spots for ERR3975966/ERR3975966.sra Written 21521182 spots for ERR3975966/ERR3975966.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170073 ("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: 01:44:51 21521182 reads; of these: 21521182 (100.00%) were paired; of these: 3323727 (15.44%) aligned concordantly 0 times 10755483 (49.98%) aligned concordantly exactly 1 time 7441972 (34.58%) aligned concordantly >1 times ---- 3323727 pairs aligned concordantly 0 times; of these: 325995 (9.81%) aligned discordantly 1 time ---- 2997732 pairs aligned 0 times concordantly or discordantly; of these: 5995464 mates make up the pairs; of these: 2539928 (42.36%) aligned 0 times 1172811 (19.56%) aligned exactly 1 time 2282725 (38.07%) aligned >1 times 94.10% overall alignment rate Time searching: 01:44:51 Overall time: 01:44:51 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] 5833080 / 18431311 = 0.3165 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 23:29:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978897/ERX3978897.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978897/ERX3978897.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978897/ERX3978897.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978897/ERX3978897.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 23:29:18: #1 read tag files... INFO @ Fri, 10 Dec 2021 23:29:18: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 23:29:26: 1000000 INFO @ Fri, 10 Dec 2021 23:29:34: 2000000 INFO @ Fri, 10 Dec 2021 23:29:43: 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 23:29:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978897/ERX3978897.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978897/ERX3978897.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978897/ERX3978897.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978897/ERX3978897.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 23:29:47: #1 read tag files... INFO @ Fri, 10 Dec 2021 23:29:47: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 23:29:51: 4000000 INFO @ Fri, 10 Dec 2021 23:29:56: 1000000 INFO @ Fri, 10 Dec 2021 23:30:01: 5000000 INFO @ Fri, 10 Dec 2021 23:30:04: 2000000 INFO @ Fri, 10 Dec 2021 23:30:11: 6000000 INFO @ Fri, 10 Dec 2021 23:30:12: 3000000 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 23:30:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX3978897/ERX3978897.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX3978897/ERX3978897.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX3978897/ERX3978897.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX3978897/ERX3978897.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 23:30:18: #1 read tag files... INFO @ Fri, 10 Dec 2021 23:30:18: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 23:30:20: 7000000 INFO @ Fri, 10 Dec 2021 23:30:21: 4000000 INFO @ Fri, 10 Dec 2021 23:30:26: 1000000 INFO @ Fri, 10 Dec 2021 23:30:29: 8000000 INFO @ Fri, 10 Dec 2021 23:30:29: 5000000 INFO @ Fri, 10 Dec 2021 23:30:35: 2000000 INFO @ Fri, 10 Dec 2021 23:30:38: 6000000 INFO @ Fri, 10 Dec 2021 23:30:39: 9000000 INFO @ Fri, 10 Dec 2021 23:30:44: 3000000 INFO @ Fri, 10 Dec 2021 23:30:47: 7000000 INFO @ Fri, 10 Dec 2021 23:30:48: 10000000 INFO @ Fri, 10 Dec 2021 23:30:53: 4000000 INFO @ Fri, 10 Dec 2021 23:30:56: 8000000 INFO @ Fri, 10 Dec 2021 23:30:57: 11000000 INFO @ Fri, 10 Dec 2021 23:31:02: 5000000 INFO @ Fri, 10 Dec 2021 23:31:05: 9000000 INFO @ Fri, 10 Dec 2021 23:31:06: 12000000 INFO @ Fri, 10 Dec 2021 23:31:11: 6000000 INFO @ Fri, 10 Dec 2021 23:31:14: 10000000 INFO @ Fri, 10 Dec 2021 23:31:16: 13000000 INFO @ Fri, 10 Dec 2021 23:31:19: 7000000 INFO @ Fri, 10 Dec 2021 23:31:22: 11000000 INFO @ Fri, 10 Dec 2021 23:31:25: 14000000 INFO @ Fri, 10 Dec 2021 23:31:28: 8000000 INFO @ Fri, 10 Dec 2021 23:31:31: 12000000 INFO @ Fri, 10 Dec 2021 23:31:34: 15000000 INFO @ Fri, 10 Dec 2021 23:31:37: 9000000 INFO @ Fri, 10 Dec 2021 23:31:40: 13000000 INFO @ Fri, 10 Dec 2021 23:31:44: 16000000 INFO @ Fri, 10 Dec 2021 23:31:46: 10000000 INFO @ Fri, 10 Dec 2021 23:31:49: 14000000 INFO @ Fri, 10 Dec 2021 23:31:53: 17000000 INFO @ Fri, 10 Dec 2021 23:31:54: 11000000 INFO @ Fri, 10 Dec 2021 23:31:57: 15000000 INFO @ Fri, 10 Dec 2021 23:32:03: 18000000 INFO @ Fri, 10 Dec 2021 23:32:03: 12000000 INFO @ Fri, 10 Dec 2021 23:32:06: 16000000 INFO @ Fri, 10 Dec 2021 23:32:12: 13000000 INFO @ Fri, 10 Dec 2021 23:32:12: 19000000 INFO @ Fri, 10 Dec 2021 23:32:15: 17000000 INFO @ Fri, 10 Dec 2021 23:32:20: 14000000 INFO @ Fri, 10 Dec 2021 23:32:22: 20000000 INFO @ Fri, 10 Dec 2021 23:32:24: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 23:32:29: 15000000 INFO @ Fri, 10 Dec 2021 23:32:32: 21000000 INFO @ Fri, 10 Dec 2021 23:32:32: 19000000 INFO @ Fri, 10 Dec 2021 23:32:38: 16000000 INFO @ Fri, 10 Dec 2021 23:32:41: 20000000 INFO @ Fri, 10 Dec 2021 23:32:41: 22000000 INFO @ Fri, 10 Dec 2021 23:32:47: 17000000 INFO @ Fri, 10 Dec 2021 23:32:50: 21000000 INFO @ Fri, 10 Dec 2021 23:32:51: 23000000 INFO @ Fri, 10 Dec 2021 23:32:55: 18000000 INFO @ Fri, 10 Dec 2021 23:32:58: 22000000 INFO @ Fri, 10 Dec 2021 23:33:00: 24000000 INFO @ Fri, 10 Dec 2021 23:33:04: 19000000 INFO @ Fri, 10 Dec 2021 23:33:07: 23000000 INFO @ Fri, 10 Dec 2021 23:33:09: 25000000 INFO @ Fri, 10 Dec 2021 23:33:13: 20000000 INFO @ Fri, 10 Dec 2021 23:33:16: 24000000 INFO @ Fri, 10 Dec 2021 23:33:18: 26000000 INFO @ Fri, 10 Dec 2021 23:33:22: 21000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 23:33:25: 25000000 INFO @ Fri, 10 Dec 2021 23:33:28: 27000000 INFO @ Fri, 10 Dec 2021 23:33:30: 22000000 INFO @ Fri, 10 Dec 2021 23:33:34: 26000000 INFO @ Fri, 10 Dec 2021 23:33:37: 28000000 INFO @ Fri, 10 Dec 2021 23:33:39: 23000000 INFO @ Fri, 10 Dec 2021 23:33:42: 27000000 INFO @ Fri, 10 Dec 2021 23:33:44: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 23:33:44: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 23:33:44: #1 total tags in treatment: 12401061 INFO @ Fri, 10 Dec 2021 23:33:44: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 23:33:44: #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 23:33:45: #1 tags after filtering in treatment: 11089390 INFO @ Fri, 10 Dec 2021 23:33:45: #1 Redundant rate of treatment: 0.11 INFO @ Fri, 10 Dec 2021 23:33:45: #1 finished! INFO @ Fri, 10 Dec 2021 23:33:45: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 23:33:45: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 23:33:45: #2 number of paired peaks: 467 WARNING @ Fri, 10 Dec 2021 23:33:45: Fewer paired peaks (467) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 467 pairs to build model! INFO @ Fri, 10 Dec 2021 23:33:45: start model_add_line... INFO @ Fri, 10 Dec 2021 23:33:45: start X-correlation... INFO @ Fri, 10 Dec 2021 23:33:46: end of X-cor INFO @ Fri, 10 Dec 2021 23:33:46: #2 finished! INFO @ Fri, 10 Dec 2021 23:33:46: #2 predicted fragment length is 145 bps INFO @ Fri, 10 Dec 2021 23:33:46: #2 alternative fragment length(s) may be 145 bps INFO @ Fri, 10 Dec 2021 23:33:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978897/ERX3978897.05_model.r WARNING @ Fri, 10 Dec 2021 23:33:46: #2 Since the d (145) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 23:33:46: #2 You may need to consider one of the other alternative d(s): 145 WARNING @ Fri, 10 Dec 2021 23:33:46: #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 23:33:46: #3 Call peaks... INFO @ Fri, 10 Dec 2021 23:33:46: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 23:33:48: 24000000 INFO @ Fri, 10 Dec 2021 23:33:51: 28000000 INFO @ Fri, 10 Dec 2021 23:33:56: 25000000 INFO @ Fri, 10 Dec 2021 23:33:57: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 23:33:57: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 23:33:57: #1 total tags in treatment: 12401061 INFO @ Fri, 10 Dec 2021 23:33:57: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 23:33:57: #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 23:33:57: #1 tags after filtering in treatment: 11089390 INFO @ Fri, 10 Dec 2021 23:33:57: #1 Redundant rate of treatment: 0.11 INFO @ Fri, 10 Dec 2021 23:33:57: #1 finished! INFO @ Fri, 10 Dec 2021 23:33:57: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 23:33:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 23:33:58: #2 number of paired peaks: 467 WARNING @ Fri, 10 Dec 2021 23:33:58: Fewer paired peaks (467) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 467 pairs to build model! INFO @ Fri, 10 Dec 2021 23:33:58: start model_add_line... INFO @ Fri, 10 Dec 2021 23:33:58: start X-correlation... INFO @ Fri, 10 Dec 2021 23:33:58: end of X-cor INFO @ Fri, 10 Dec 2021 23:33:58: #2 finished! INFO @ Fri, 10 Dec 2021 23:33:58: #2 predicted fragment length is 145 bps INFO @ Fri, 10 Dec 2021 23:33:58: #2 alternative fragment length(s) may be 145 bps INFO @ Fri, 10 Dec 2021 23:33:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978897/ERX3978897.10_model.r WARNING @ Fri, 10 Dec 2021 23:33:58: #2 Since the d (145) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 23:33:58: #2 You may need to consider one of the other alternative d(s): 145 WARNING @ Fri, 10 Dec 2021 23:33:58: #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 23:33:58: #3 Call peaks... INFO @ Fri, 10 Dec 2021 23:33:58: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 23:34:04: 26000000 INFO @ Fri, 10 Dec 2021 23:34:08: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 23:34:11: 27000000 INFO @ Fri, 10 Dec 2021 23:34:18: 28000000 INFO @ Fri, 10 Dec 2021 23:34:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978897/ERX3978897.05_peaks.xls INFO @ Fri, 10 Dec 2021 23:34:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978897/ERX3978897.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 23:34:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978897/ERX3978897.05_summits.bed INFO @ Fri, 10 Dec 2021 23:34:19: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6695 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 23:34:21: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 23:34:24: #1 tag size is determined as 80 bps INFO @ Fri, 10 Dec 2021 23:34:24: #1 tag size = 80 INFO @ Fri, 10 Dec 2021 23:34:24: #1 total tags in treatment: 12401061 INFO @ Fri, 10 Dec 2021 23:34:24: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 23:34:24: #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 23:34:24: #1 tags after filtering in treatment: 11089390 INFO @ Fri, 10 Dec 2021 23:34:24: #1 Redundant rate of treatment: 0.11 INFO @ Fri, 10 Dec 2021 23:34:24: #1 finished! INFO @ Fri, 10 Dec 2021 23:34:24: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 23:34:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 23:34:25: #2 number of paired peaks: 467 WARNING @ Fri, 10 Dec 2021 23:34:25: Fewer paired peaks (467) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 467 pairs to build model! INFO @ Fri, 10 Dec 2021 23:34:25: start model_add_line... INFO @ Fri, 10 Dec 2021 23:34:25: start X-correlation... INFO @ Fri, 10 Dec 2021 23:34:25: end of X-cor INFO @ Fri, 10 Dec 2021 23:34:25: #2 finished! INFO @ Fri, 10 Dec 2021 23:34:25: #2 predicted fragment length is 145 bps INFO @ Fri, 10 Dec 2021 23:34:25: #2 alternative fragment length(s) may be 145 bps INFO @ Fri, 10 Dec 2021 23:34:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX3978897/ERX3978897.20_model.r WARNING @ Fri, 10 Dec 2021 23:34:25: #2 Since the d (145) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 23:34:25: #2 You may need to consider one of the other alternative d(s): 145 WARNING @ Fri, 10 Dec 2021 23:34:25: #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 23:34:25: #3 Call peaks... INFO @ Fri, 10 Dec 2021 23:34:25: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 23:34:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978897/ERX3978897.10_peaks.xls INFO @ Fri, 10 Dec 2021 23:34:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978897/ERX3978897.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 23:34:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978897/ERX3978897.10_summits.bed INFO @ Fri, 10 Dec 2021 23:34:32: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3572 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 23:34:48: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 23:34:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX3978897/ERX3978897.20_peaks.xls INFO @ Fri, 10 Dec 2021 23:34:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX3978897/ERX3978897.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 23:34:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX3978897/ERX3978897.20_summits.bed INFO @ Fri, 10 Dec 2021 23:34:58: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1493 records, 4 fields): 3 millis CompletedMACS2peakCalling