Job ID = 12266618 SRX = SRX7351029 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 17128443 spots for SRR10673659/SRR10673659.sra Written 17128443 spots for SRR10673659/SRR10673659.sra fastq に変換しました。 bowtie でマッピング中... Your job 12267241 ("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: 00:41:35 17128443 reads; of these: 17128443 (100.00%) were paired; of these: 7883569 (46.03%) aligned concordantly 0 times 5711143 (33.34%) aligned concordantly exactly 1 time 3533731 (20.63%) aligned concordantly >1 times ---- 7883569 pairs aligned concordantly 0 times; of these: 1350821 (17.13%) aligned discordantly 1 time ---- 6532748 pairs aligned 0 times concordantly or discordantly; of these: 13065496 mates make up the pairs; of these: 11091990 (84.90%) aligned 0 times 429691 (3.29%) aligned exactly 1 time 1543815 (11.82%) aligned >1 times 67.62% overall alignment rate Time searching: 00:41:35 Overall time: 00:41:35 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 12 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] 1273603 / 10464606 = 0.1217 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 09:54:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7351029/SRX7351029.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7351029/SRX7351029.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7351029/SRX7351029.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7351029/SRX7351029.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, 03 Apr 2021 09:54:04: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:54:04: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:54:10: 1000000 INFO @ Sat, 03 Apr 2021 09:54:16: 2000000 INFO @ Sat, 03 Apr 2021 09:54:22: 3000000 INFO @ Sat, 03 Apr 2021 09:54:29: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 09:54:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7351029/SRX7351029.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7351029/SRX7351029.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7351029/SRX7351029.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7351029/SRX7351029.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, 03 Apr 2021 09:54:34: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:54:34: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:54:35: 5000000 INFO @ Sat, 03 Apr 2021 09:54:41: 1000000 INFO @ Sat, 03 Apr 2021 09:54:42: 6000000 INFO @ Sat, 03 Apr 2021 09:54:48: 2000000 INFO @ Sat, 03 Apr 2021 09:54:49: 7000000 INFO @ Sat, 03 Apr 2021 09:54:55: 3000000 INFO @ Sat, 03 Apr 2021 09:54:56: 8000000 INFO @ Sat, 03 Apr 2021 09:55:02: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 09:55:03: 9000000 INFO @ Sat, 03 Apr 2021 09:55:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7351029/SRX7351029.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7351029/SRX7351029.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7351029/SRX7351029.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7351029/SRX7351029.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, 03 Apr 2021 09:55:04: #1 read tag files... INFO @ Sat, 03 Apr 2021 09:55:04: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 09:55:09: 5000000 INFO @ Sat, 03 Apr 2021 09:55:10: 10000000 INFO @ Sat, 03 Apr 2021 09:55:12: 1000000 INFO @ Sat, 03 Apr 2021 09:55:16: 6000000 INFO @ Sat, 03 Apr 2021 09:55:18: 11000000 INFO @ Sat, 03 Apr 2021 09:55:19: 2000000 INFO @ Sat, 03 Apr 2021 09:55:24: 7000000 INFO @ Sat, 03 Apr 2021 09:55:25: 12000000 INFO @ Sat, 03 Apr 2021 09:55:26: 3000000 INFO @ Sat, 03 Apr 2021 09:55:31: 8000000 INFO @ Sat, 03 Apr 2021 09:55:32: 13000000 INFO @ Sat, 03 Apr 2021 09:55:34: 4000000 INFO @ Sat, 03 Apr 2021 09:55:39: 9000000 INFO @ Sat, 03 Apr 2021 09:55:40: 14000000 INFO @ Sat, 03 Apr 2021 09:55:41: 5000000 INFO @ Sat, 03 Apr 2021 09:55:46: 10000000 INFO @ Sat, 03 Apr 2021 09:55:46: 15000000 INFO @ Sat, 03 Apr 2021 09:55:49: 6000000 INFO @ Sat, 03 Apr 2021 09:55:54: 16000000 INFO @ Sat, 03 Apr 2021 09:55:54: 11000000 INFO @ Sat, 03 Apr 2021 09:55:56: 7000000 INFO @ Sat, 03 Apr 2021 09:56:01: 17000000 INFO @ Sat, 03 Apr 2021 09:56:01: 12000000 INFO @ Sat, 03 Apr 2021 09:56:04: 8000000 INFO @ Sat, 03 Apr 2021 09:56:09: 18000000 INFO @ Sat, 03 Apr 2021 09:56:09: 13000000 INFO @ Sat, 03 Apr 2021 09:56:12: 9000000 INFO @ Sat, 03 Apr 2021 09:56:16: 19000000 INFO @ Sat, 03 Apr 2021 09:56:17: 14000000 INFO @ Sat, 03 Apr 2021 09:56:20: 10000000 INFO @ Sat, 03 Apr 2021 09:56:24: 15000000 INFO @ Sat, 03 Apr 2021 09:56:24: 20000000 INFO @ Sat, 03 Apr 2021 09:56:27: 11000000 INFO @ Sat, 03 Apr 2021 09:56:28: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 09:56:28: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 09:56:28: #1 total tags in treatment: 8060603 INFO @ Sat, 03 Apr 2021 09:56:28: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:56:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 09:56:28: #1 tags after filtering in treatment: 7007289 INFO @ Sat, 03 Apr 2021 09:56:28: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 03 Apr 2021 09:56:28: #1 finished! INFO @ Sat, 03 Apr 2021 09:56:28: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:56:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 09:56:29: #2 number of paired peaks: 593 WARNING @ Sat, 03 Apr 2021 09:56:29: Fewer paired peaks (593) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 593 pairs to build model! INFO @ Sat, 03 Apr 2021 09:56:29: start model_add_line... INFO @ Sat, 03 Apr 2021 09:56:29: start X-correlation... INFO @ Sat, 03 Apr 2021 09:56:29: end of X-cor INFO @ Sat, 03 Apr 2021 09:56:29: #2 finished! INFO @ Sat, 03 Apr 2021 09:56:29: #2 predicted fragment length is 126 bps INFO @ Sat, 03 Apr 2021 09:56:29: #2 alternative fragment length(s) may be 126,578,593 bps INFO @ Sat, 03 Apr 2021 09:56:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7351029/SRX7351029.05_model.r WARNING @ Sat, 03 Apr 2021 09:56:29: #2 Since the d (126) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 09:56:29: #2 You may need to consider one of the other alternative d(s): 126,578,593 WARNING @ Sat, 03 Apr 2021 09:56:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 09:56:29: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:56:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 09:56:31: 16000000 INFO @ Sat, 03 Apr 2021 09:56:35: 12000000 INFO @ Sat, 03 Apr 2021 09:56:38: 17000000 INFO @ Sat, 03 Apr 2021 09:56:42: 13000000 INFO @ Sat, 03 Apr 2021 09:56:44: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 09:56:45: 18000000 INFO @ Sat, 03 Apr 2021 09:56:49: 14000000 INFO @ Sat, 03 Apr 2021 09:56:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7351029/SRX7351029.05_peaks.xls INFO @ Sat, 03 Apr 2021 09:56:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7351029/SRX7351029.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:56:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7351029/SRX7351029.05_summits.bed INFO @ Sat, 03 Apr 2021 09:56:51: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2301 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 09:56:52: 19000000 INFO @ Sat, 03 Apr 2021 09:56:55: 15000000 INFO @ Sat, 03 Apr 2021 09:57:00: 20000000 INFO @ Sat, 03 Apr 2021 09:57:02: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 09:57:04: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 09:57:04: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 09:57:04: #1 total tags in treatment: 8060603 INFO @ Sat, 03 Apr 2021 09:57:04: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:57:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 09:57:04: #1 tags after filtering in treatment: 7007289 INFO @ Sat, 03 Apr 2021 09:57:04: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 03 Apr 2021 09:57:04: #1 finished! INFO @ Sat, 03 Apr 2021 09:57:04: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:57:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 09:57:05: #2 number of paired peaks: 593 WARNING @ Sat, 03 Apr 2021 09:57:05: Fewer paired peaks (593) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 593 pairs to build model! INFO @ Sat, 03 Apr 2021 09:57:05: start model_add_line... INFO @ Sat, 03 Apr 2021 09:57:05: start X-correlation... INFO @ Sat, 03 Apr 2021 09:57:05: end of X-cor INFO @ Sat, 03 Apr 2021 09:57:05: #2 finished! INFO @ Sat, 03 Apr 2021 09:57:05: #2 predicted fragment length is 126 bps INFO @ Sat, 03 Apr 2021 09:57:05: #2 alternative fragment length(s) may be 126,578,593 bps INFO @ Sat, 03 Apr 2021 09:57:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7351029/SRX7351029.10_model.r WARNING @ Sat, 03 Apr 2021 09:57:05: #2 Since the d (126) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 09:57:05: #2 You may need to consider one of the other alternative d(s): 126,578,593 WARNING @ Sat, 03 Apr 2021 09:57:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 09:57:05: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:57:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 09:57:08: 17000000 INFO @ Sat, 03 Apr 2021 09:57:15: 18000000 INFO @ Sat, 03 Apr 2021 09:57:19: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 09:57:21: 19000000 INFO @ Sat, 03 Apr 2021 09:57:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7351029/SRX7351029.10_peaks.xls INFO @ Sat, 03 Apr 2021 09:57:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7351029/SRX7351029.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:57:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7351029/SRX7351029.10_summits.bed INFO @ Sat, 03 Apr 2021 09:57:27: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1160 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 09:57:28: 20000000 INFO @ Sat, 03 Apr 2021 09:57:31: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 09:57:31: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 09:57:31: #1 total tags in treatment: 8060603 INFO @ Sat, 03 Apr 2021 09:57:31: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 09:57:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 09:57:32: #1 tags after filtering in treatment: 7007289 INFO @ Sat, 03 Apr 2021 09:57:32: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 03 Apr 2021 09:57:32: #1 finished! INFO @ Sat, 03 Apr 2021 09:57:32: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 09:57:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 09:57:32: #2 number of paired peaks: 593 WARNING @ Sat, 03 Apr 2021 09:57:32: Fewer paired peaks (593) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 593 pairs to build model! INFO @ Sat, 03 Apr 2021 09:57:32: start model_add_line... INFO @ Sat, 03 Apr 2021 09:57:32: start X-correlation... INFO @ Sat, 03 Apr 2021 09:57:32: end of X-cor INFO @ Sat, 03 Apr 2021 09:57:32: #2 finished! INFO @ Sat, 03 Apr 2021 09:57:32: #2 predicted fragment length is 126 bps INFO @ Sat, 03 Apr 2021 09:57:32: #2 alternative fragment length(s) may be 126,578,593 bps INFO @ Sat, 03 Apr 2021 09:57:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7351029/SRX7351029.20_model.r WARNING @ Sat, 03 Apr 2021 09:57:32: #2 Since the d (126) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 09:57:32: #2 You may need to consider one of the other alternative d(s): 126,578,593 WARNING @ Sat, 03 Apr 2021 09:57:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 09:57:32: #3 Call peaks... INFO @ Sat, 03 Apr 2021 09:57:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 09:57:47: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 09:57:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7351029/SRX7351029.20_peaks.xls INFO @ Sat, 03 Apr 2021 09:57:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7351029/SRX7351029.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 09:57:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7351029/SRX7351029.20_summits.bed INFO @ Sat, 03 Apr 2021 09:57:54: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (430 records, 4 fields): 2 millis CompletedMACS2peakCalling