Job ID = 16439496 SRX = SRX9518328 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 7702531 spots for SRR13070811/SRR13070811.sra Written 7702531 spots for SRR13070811/SRR13070811.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439674 ("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: 00:25:35 7702531 reads; of these: 7702531 (100.00%) were paired; of these: 488869 (6.35%) aligned concordantly 0 times 5369360 (69.71%) aligned concordantly exactly 1 time 1844302 (23.94%) aligned concordantly >1 times ---- 488869 pairs aligned concordantly 0 times; of these: 181938 (37.22%) aligned discordantly 1 time ---- 306931 pairs aligned 0 times concordantly or discordantly; of these: 613862 mates make up the pairs; of these: 339256 (55.27%) aligned 0 times 120601 (19.65%) aligned exactly 1 time 154005 (25.09%) aligned >1 times 97.80% overall alignment rate Time searching: 00:25:35 Overall time: 00:25:35 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 8 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] 125728 / 7367879 = 0.0171 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 15:54:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9518328/SRX9518328.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9518328/SRX9518328.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9518328/SRX9518328.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9518328/SRX9518328.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 @ Tue, 02 Aug 2022 15:54:50: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:54:50: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:55:00: 1000000 INFO @ Tue, 02 Aug 2022 15:55:10: 2000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 15:55:19: 3000000 INFO @ Tue, 02 Aug 2022 15:55:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9518328/SRX9518328.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9518328/SRX9518328.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9518328/SRX9518328.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9518328/SRX9518328.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 @ Tue, 02 Aug 2022 15:55:20: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:55:20: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:55:27: 1000000 INFO @ Tue, 02 Aug 2022 15:55:29: 4000000 INFO @ Tue, 02 Aug 2022 15:55:33: 2000000 INFO @ Tue, 02 Aug 2022 15:55:38: 5000000 INFO @ Tue, 02 Aug 2022 15:55:40: 3000000 INFO @ Tue, 02 Aug 2022 15:55:46: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 15:55:48: 6000000 INFO @ Tue, 02 Aug 2022 15:55:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9518328/SRX9518328.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9518328/SRX9518328.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9518328/SRX9518328.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9518328/SRX9518328.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 @ Tue, 02 Aug 2022 15:55:50: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:55:50: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:55:53: 5000000 INFO @ Tue, 02 Aug 2022 15:55:57: 7000000 INFO @ Tue, 02 Aug 2022 15:55:58: 1000000 INFO @ Tue, 02 Aug 2022 15:56:01: 6000000 INFO @ Tue, 02 Aug 2022 15:56:06: 2000000 INFO @ Tue, 02 Aug 2022 15:56:06: 8000000 INFO @ Tue, 02 Aug 2022 15:56:08: 7000000 INFO @ Tue, 02 Aug 2022 15:56:14: 3000000 INFO @ Tue, 02 Aug 2022 15:56:15: 8000000 INFO @ Tue, 02 Aug 2022 15:56:15: 9000000 INFO @ Tue, 02 Aug 2022 15:56:21: 4000000 INFO @ Tue, 02 Aug 2022 15:56:22: 9000000 INFO @ Tue, 02 Aug 2022 15:56:25: 10000000 INFO @ Tue, 02 Aug 2022 15:56:29: 5000000 INFO @ Tue, 02 Aug 2022 15:56:30: 10000000 INFO @ Tue, 02 Aug 2022 15:56:34: 11000000 INFO @ Tue, 02 Aug 2022 15:56:36: 6000000 INFO @ Tue, 02 Aug 2022 15:56:37: 11000000 INFO @ Tue, 02 Aug 2022 15:56:43: 7000000 INFO @ Tue, 02 Aug 2022 15:56:43: 12000000 INFO @ Tue, 02 Aug 2022 15:56:44: 12000000 INFO @ Tue, 02 Aug 2022 15:56:51: 8000000 INFO @ Tue, 02 Aug 2022 15:56:52: 13000000 INFO @ Tue, 02 Aug 2022 15:56:52: 13000000 INFO @ Tue, 02 Aug 2022 15:56:58: 9000000 INFO @ Tue, 02 Aug 2022 15:56:59: 14000000 INFO @ Tue, 02 Aug 2022 15:57:01: 14000000 INFO @ Tue, 02 Aug 2022 15:57:06: 10000000 INFO @ Tue, 02 Aug 2022 15:57:06: #1 tag size is determined as 101 bps INFO @ Tue, 02 Aug 2022 15:57:06: #1 tag size = 101 INFO @ Tue, 02 Aug 2022 15:57:06: #1 total tags in treatment: 7089481 INFO @ Tue, 02 Aug 2022 15:57:06: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:57:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 15:57:06: #1 tags after filtering in treatment: 6860864 INFO @ Tue, 02 Aug 2022 15:57:06: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 02 Aug 2022 15:57:06: #1 finished! INFO @ Tue, 02 Aug 2022 15:57:06: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:57:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:57:06: #2 number of paired peaks: 115 WARNING @ Tue, 02 Aug 2022 15:57:06: Fewer paired peaks (115) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 115 pairs to build model! INFO @ Tue, 02 Aug 2022 15:57:06: start model_add_line... INFO @ Tue, 02 Aug 2022 15:57:06: start X-correlation... INFO @ Tue, 02 Aug 2022 15:57:06: end of X-cor INFO @ Tue, 02 Aug 2022 15:57:06: #2 finished! INFO @ Tue, 02 Aug 2022 15:57:06: #2 predicted fragment length is 150 bps INFO @ Tue, 02 Aug 2022 15:57:06: #2 alternative fragment length(s) may be 150 bps INFO @ Tue, 02 Aug 2022 15:57:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9518328/SRX9518328.10_model.r WARNING @ Tue, 02 Aug 2022 15:57:06: #2 Since the d (150) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:57:06: #2 You may need to consider one of the other alternative d(s): 150 WARNING @ Tue, 02 Aug 2022 15:57:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 15:57:06: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:57:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:57:08: #1 tag size is determined as 101 bps INFO @ Tue, 02 Aug 2022 15:57:08: #1 tag size = 101 INFO @ Tue, 02 Aug 2022 15:57:08: #1 total tags in treatment: 7089481 INFO @ Tue, 02 Aug 2022 15:57:08: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:57:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 15:57:08: #1 tags after filtering in treatment: 6860864 INFO @ Tue, 02 Aug 2022 15:57:08: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 02 Aug 2022 15:57:08: #1 finished! INFO @ Tue, 02 Aug 2022 15:57:08: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:57:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:57:09: #2 number of paired peaks: 115 WARNING @ Tue, 02 Aug 2022 15:57:09: Fewer paired peaks (115) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 115 pairs to build model! INFO @ Tue, 02 Aug 2022 15:57:09: start model_add_line... INFO @ Tue, 02 Aug 2022 15:57:09: start X-correlation... INFO @ Tue, 02 Aug 2022 15:57:09: end of X-cor INFO @ Tue, 02 Aug 2022 15:57:09: #2 finished! INFO @ Tue, 02 Aug 2022 15:57:09: #2 predicted fragment length is 150 bps INFO @ Tue, 02 Aug 2022 15:57:09: #2 alternative fragment length(s) may be 150 bps INFO @ Tue, 02 Aug 2022 15:57:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9518328/SRX9518328.05_model.r WARNING @ Tue, 02 Aug 2022 15:57:09: #2 Since the d (150) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:57:09: #2 You may need to consider one of the other alternative d(s): 150 WARNING @ Tue, 02 Aug 2022 15:57:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 15:57:09: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:57:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:57:13: 11000000 INFO @ Tue, 02 Aug 2022 15:57:19: 12000000 INFO @ Tue, 02 Aug 2022 15:57:19: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:57:22: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:57:26: 13000000 INFO @ Tue, 02 Aug 2022 15:57:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9518328/SRX9518328.10_peaks.xls INFO @ Tue, 02 Aug 2022 15:57:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9518328/SRX9518328.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:57:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9518328/SRX9518328.10_summits.bed INFO @ Tue, 02 Aug 2022 15:57:26: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (415 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:57:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9518328/SRX9518328.05_peaks.xls INFO @ Tue, 02 Aug 2022 15:57:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9518328/SRX9518328.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:57:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9518328/SRX9518328.05_summits.bed INFO @ Tue, 02 Aug 2022 15:57:29: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (817 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:57:32: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 15:57:37: #1 tag size is determined as 101 bps INFO @ Tue, 02 Aug 2022 15:57:37: #1 tag size = 101 INFO @ Tue, 02 Aug 2022 15:57:37: #1 total tags in treatment: 7089481 INFO @ Tue, 02 Aug 2022 15:57:37: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:57:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 15:57:37: #1 tags after filtering in treatment: 6860864 INFO @ Tue, 02 Aug 2022 15:57:37: #1 Redundant rate of treatment: 0.03 INFO @ Tue, 02 Aug 2022 15:57:37: #1 finished! INFO @ Tue, 02 Aug 2022 15:57:37: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:57:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:57:38: #2 number of paired peaks: 115 WARNING @ Tue, 02 Aug 2022 15:57:38: Fewer paired peaks (115) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 115 pairs to build model! INFO @ Tue, 02 Aug 2022 15:57:38: start model_add_line... INFO @ Tue, 02 Aug 2022 15:57:38: start X-correlation... INFO @ Tue, 02 Aug 2022 15:57:38: end of X-cor INFO @ Tue, 02 Aug 2022 15:57:38: #2 finished! INFO @ Tue, 02 Aug 2022 15:57:38: #2 predicted fragment length is 150 bps INFO @ Tue, 02 Aug 2022 15:57:38: #2 alternative fragment length(s) may be 150 bps INFO @ Tue, 02 Aug 2022 15:57:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9518328/SRX9518328.20_model.r WARNING @ Tue, 02 Aug 2022 15:57:38: #2 Since the d (150) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:57:38: #2 You may need to consider one of the other alternative d(s): 150 WARNING @ Tue, 02 Aug 2022 15:57:38: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 15:57:38: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:57:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:57:51: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:57:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9518328/SRX9518328.20_peaks.xls INFO @ Tue, 02 Aug 2022 15:57:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9518328/SRX9518328.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:57:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9518328/SRX9518328.20_summits.bed INFO @ Tue, 02 Aug 2022 15:57:58: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (197 records, 4 fields): 15 millis CompletedMACS2peakCalling BigWig に変換しました。