Job ID = 16439450 SRX = SRX9518312 Genome = dm3 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 17853488 spots for SRR13070795/SRR13070795.sra Written 17853488 spots for SRR13070795/SRR13070795.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439653 ("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: 00:31:43 17853488 reads; of these: 17853488 (100.00%) were paired; of these: 3493294 (19.57%) aligned concordantly 0 times 6308380 (35.33%) aligned concordantly exactly 1 time 8051814 (45.10%) aligned concordantly >1 times ---- 3493294 pairs aligned concordantly 0 times; of these: 639937 (18.32%) aligned discordantly 1 time ---- 2853357 pairs aligned 0 times concordantly or discordantly; of these: 5706714 mates make up the pairs; of these: 4070249 (71.32%) aligned 0 times 275929 (4.84%) aligned exactly 1 time 1360536 (23.84%) aligned >1 times 88.60% overall alignment rate Time searching: 00:31:43 Overall time: 00:31:43 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 16 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] 5033370 / 14878313 = 0.3383 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 15:55:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9518312/SRX9518312.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9518312/SRX9518312.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9518312/SRX9518312.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9518312/SRX9518312.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 15:55:56: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:55:56: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:56:03: 1000000 INFO @ Tue, 02 Aug 2022 15:56:09: 2000000 INFO @ Tue, 02 Aug 2022 15:56:16: 3000000 INFO @ Tue, 02 Aug 2022 15:56:23: 4000000 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 15:56:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9518312/SRX9518312.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9518312/SRX9518312.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9518312/SRX9518312.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9518312/SRX9518312.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 15:56:25: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:56:25: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:56:30: 5000000 INFO @ Tue, 02 Aug 2022 15:56:33: 1000000 INFO @ Tue, 02 Aug 2022 15:56:38: 6000000 INFO @ Tue, 02 Aug 2022 15:56:40: 2000000 INFO @ Tue, 02 Aug 2022 15:56:45: 7000000 INFO @ Tue, 02 Aug 2022 15:56:48: 3000000 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 15:56:53: 8000000 INFO @ Tue, 02 Aug 2022 15:56:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9518312/SRX9518312.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9518312/SRX9518312.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9518312/SRX9518312.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9518312/SRX9518312.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 15:56:55: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:56:55: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:56:55: 4000000 INFO @ Tue, 02 Aug 2022 15:57:01: 9000000 INFO @ Tue, 02 Aug 2022 15:57:03: 1000000 INFO @ Tue, 02 Aug 2022 15:57:03: 5000000 INFO @ Tue, 02 Aug 2022 15:57:09: 10000000 INFO @ Tue, 02 Aug 2022 15:57:11: 2000000 INFO @ Tue, 02 Aug 2022 15:57:11: 6000000 INFO @ Tue, 02 Aug 2022 15:57:17: 11000000 INFO @ Tue, 02 Aug 2022 15:57:18: 3000000 INFO @ Tue, 02 Aug 2022 15:57:18: 7000000 INFO @ Tue, 02 Aug 2022 15:57:25: 12000000 INFO @ Tue, 02 Aug 2022 15:57:26: 4000000 INFO @ Tue, 02 Aug 2022 15:57:26: 8000000 INFO @ Tue, 02 Aug 2022 15:57:33: 13000000 INFO @ Tue, 02 Aug 2022 15:57:34: 5000000 INFO @ Tue, 02 Aug 2022 15:57:34: 9000000 INFO @ Tue, 02 Aug 2022 15:57:40: 14000000 INFO @ Tue, 02 Aug 2022 15:57:42: 6000000 INFO @ Tue, 02 Aug 2022 15:57:42: 10000000 INFO @ Tue, 02 Aug 2022 15:57:48: 15000000 INFO @ Tue, 02 Aug 2022 15:57:49: 7000000 INFO @ Tue, 02 Aug 2022 15:57:50: 11000000 INFO @ Tue, 02 Aug 2022 15:57:55: 16000000 INFO @ Tue, 02 Aug 2022 15:57:57: 8000000 INFO @ Tue, 02 Aug 2022 15:57:58: 12000000 INFO @ Tue, 02 Aug 2022 15:58:03: 17000000 INFO @ Tue, 02 Aug 2022 15:58:05: 9000000 INFO @ Tue, 02 Aug 2022 15:58:06: 13000000 INFO @ Tue, 02 Aug 2022 15:58:12: 18000000 INFO @ Tue, 02 Aug 2022 15:58:13: 10000000 INFO @ Tue, 02 Aug 2022 15:58:14: 14000000 INFO @ Tue, 02 Aug 2022 15:58:20: 19000000 INFO @ Tue, 02 Aug 2022 15:58:21: 15000000 INFO @ Tue, 02 Aug 2022 15:58:21: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 15:58:28: 20000000 INFO @ Tue, 02 Aug 2022 15:58:29: 16000000 INFO @ Tue, 02 Aug 2022 15:58:30: 12000000 INFO @ Tue, 02 Aug 2022 15:58:36: 21000000 INFO @ Tue, 02 Aug 2022 15:58:37: 17000000 INFO @ Tue, 02 Aug 2022 15:58:38: 13000000 INFO @ Tue, 02 Aug 2022 15:58:41: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 15:58:41: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 15:58:41: #1 total tags in treatment: 9349639 INFO @ Tue, 02 Aug 2022 15:58:41: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:58:41: #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 15:58:41: #1 tags after filtering in treatment: 7373500 INFO @ Tue, 02 Aug 2022 15:58:41: #1 Redundant rate of treatment: 0.21 INFO @ Tue, 02 Aug 2022 15:58:41: #1 finished! INFO @ Tue, 02 Aug 2022 15:58:41: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:58:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:58:41: #2 number of paired peaks: 597 WARNING @ Tue, 02 Aug 2022 15:58:41: Fewer paired peaks (597) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 597 pairs to build model! INFO @ Tue, 02 Aug 2022 15:58:41: start model_add_line... INFO @ Tue, 02 Aug 2022 15:58:42: start X-correlation... INFO @ Tue, 02 Aug 2022 15:58:42: end of X-cor INFO @ Tue, 02 Aug 2022 15:58:42: #2 finished! INFO @ Tue, 02 Aug 2022 15:58:42: #2 predicted fragment length is 118 bps INFO @ Tue, 02 Aug 2022 15:58:42: #2 alternative fragment length(s) may be 118 bps INFO @ Tue, 02 Aug 2022 15:58:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9518312/SRX9518312.05_model.r WARNING @ Tue, 02 Aug 2022 15:58:42: #2 Since the d (118) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:58:42: #2 You may need to consider one of the other alternative d(s): 118 WARNING @ Tue, 02 Aug 2022 15:58:42: #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 15:58:42: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:58:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:58:45: 18000000 INFO @ Tue, 02 Aug 2022 15:58:46: 14000000 INFO @ Tue, 02 Aug 2022 15:58:53: 15000000 INFO @ Tue, 02 Aug 2022 15:58:53: 19000000 INFO @ Tue, 02 Aug 2022 15:58:58: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:59:00: 16000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 15:59:01: 20000000 INFO @ Tue, 02 Aug 2022 15:59:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9518312/SRX9518312.05_peaks.xls INFO @ Tue, 02 Aug 2022 15:59:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9518312/SRX9518312.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:59:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9518312/SRX9518312.05_summits.bed INFO @ Tue, 02 Aug 2022 15:59:06: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4880 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:59:08: 17000000 INFO @ Tue, 02 Aug 2022 15:59:09: 21000000 INFO @ Tue, 02 Aug 2022 15:59:14: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 15:59:14: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 15:59:14: #1 total tags in treatment: 9349639 INFO @ Tue, 02 Aug 2022 15:59:14: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:59:14: #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 15:59:14: #1 tags after filtering in treatment: 7373500 INFO @ Tue, 02 Aug 2022 15:59:14: #1 Redundant rate of treatment: 0.21 INFO @ Tue, 02 Aug 2022 15:59:14: #1 finished! INFO @ Tue, 02 Aug 2022 15:59:14: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:59:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:59:14: #2 number of paired peaks: 597 WARNING @ Tue, 02 Aug 2022 15:59:14: Fewer paired peaks (597) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 597 pairs to build model! INFO @ Tue, 02 Aug 2022 15:59:14: start model_add_line... INFO @ Tue, 02 Aug 2022 15:59:14: start X-correlation... INFO @ Tue, 02 Aug 2022 15:59:14: end of X-cor INFO @ Tue, 02 Aug 2022 15:59:14: #2 finished! INFO @ Tue, 02 Aug 2022 15:59:14: #2 predicted fragment length is 118 bps INFO @ Tue, 02 Aug 2022 15:59:14: #2 alternative fragment length(s) may be 118 bps INFO @ Tue, 02 Aug 2022 15:59:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9518312/SRX9518312.10_model.r WARNING @ Tue, 02 Aug 2022 15:59:14: #2 Since the d (118) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:59:14: #2 You may need to consider one of the other alternative d(s): 118 WARNING @ Tue, 02 Aug 2022 15:59:14: #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 15:59:14: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:59:14: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:59:16: 18000000 INFO @ Tue, 02 Aug 2022 15:59:22: 19000000 INFO @ Tue, 02 Aug 2022 15:59:29: 20000000 INFO @ Tue, 02 Aug 2022 15:59:31: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:59:35: 21000000 INFO @ Tue, 02 Aug 2022 15:59:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9518312/SRX9518312.10_peaks.xls INFO @ Tue, 02 Aug 2022 15:59:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9518312/SRX9518312.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:59:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9518312/SRX9518312.10_summits.bed INFO @ Tue, 02 Aug 2022 15:59:39: Done! INFO @ Tue, 02 Aug 2022 15:59:39: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 15:59:39: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 15:59:39: #1 total tags in treatment: 9349639 INFO @ Tue, 02 Aug 2022 15:59:39: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:59:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass1 - making usageList (13 chroms): 1 millis INFO @ Tue, 02 Aug 2022 15:59:39: #1 tags after filtering in treatment: 7373500 INFO @ Tue, 02 Aug 2022 15:59:39: #1 Redundant rate of treatment: 0.21 INFO @ Tue, 02 Aug 2022 15:59:39: #1 finished! INFO @ Tue, 02 Aug 2022 15:59:39: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:59:39: #2 looking for paired plus/minus strand peaks... pass2 - checking and writing primary data (1797 records, 4 fields): 59 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:59:40: #2 number of paired peaks: 597 WARNING @ Tue, 02 Aug 2022 15:59:40: Fewer paired peaks (597) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 597 pairs to build model! INFO @ Tue, 02 Aug 2022 15:59:40: start model_add_line... INFO @ Tue, 02 Aug 2022 15:59:40: start X-correlation... INFO @ Tue, 02 Aug 2022 15:59:40: end of X-cor INFO @ Tue, 02 Aug 2022 15:59:40: #2 finished! INFO @ Tue, 02 Aug 2022 15:59:40: #2 predicted fragment length is 118 bps INFO @ Tue, 02 Aug 2022 15:59:40: #2 alternative fragment length(s) may be 118 bps INFO @ Tue, 02 Aug 2022 15:59:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9518312/SRX9518312.20_model.r WARNING @ Tue, 02 Aug 2022 15:59:40: #2 Since the d (118) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:59:40: #2 You may need to consider one of the other alternative d(s): 118 WARNING @ Tue, 02 Aug 2022 15:59:40: #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 15:59:40: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:59:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:59:55: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:00:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9518312/SRX9518312.20_peaks.xls INFO @ Tue, 02 Aug 2022 16:00:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9518312/SRX9518312.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:00:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9518312/SRX9518312.20_summits.bed INFO @ Tue, 02 Aug 2022 16:00:03: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (606 records, 4 fields): 19 millis CompletedMACS2peakCalling