Job ID = 16439162 SRX = SRX15206451 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T05:41:01 prefetch.2.10.7: 1) Downloading 'SRR19139355'... 2022-08-02T05:41:01 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T05:41:09 prefetch.2.10.7: HTTPS download succeed 2022-08-02T05:41:09 prefetch.2.10.7: 'SRR19139355' is valid 2022-08-02T05:41:09 prefetch.2.10.7: 1) 'SRR19139355' was downloaded successfully 2022-08-02T05:41:09 prefetch.2.10.7: 'SRR19139355' has 0 unresolved dependencies Read 2036335 spots for SRR19139355/SRR19139355.sra Written 2036335 spots for SRR19139355/SRR19139355.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439183 ("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: 00:01:20 2036335 reads; of these: 2036335 (100.00%) were unpaired; of these: 768619 (37.75%) aligned 0 times 941090 (46.21%) aligned exactly 1 time 326626 (16.04%) aligned >1 times 62.25% overall alignment rate Time searching: 00:01:20 Overall time: 00:01:20 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_rmdupse_core] 262734 / 1267716 = 0.2072 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 14:43:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206451/SRX15206451.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206451/SRX15206451.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206451/SRX15206451.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206451/SRX15206451.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 14:43:44: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:43:44: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:43:51: 1000000 INFO @ Tue, 02 Aug 2022 14:43:51: #1 tag size is determined as 100 bps INFO @ Tue, 02 Aug 2022 14:43:51: #1 tag size = 100 INFO @ Tue, 02 Aug 2022 14:43:51: #1 total tags in treatment: 1004982 INFO @ Tue, 02 Aug 2022 14:43:51: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:43:51: #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 14:43:51: #1 tags after filtering in treatment: 1004982 INFO @ Tue, 02 Aug 2022 14:43:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:43:51: #1 finished! INFO @ Tue, 02 Aug 2022 14:43:51: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:43:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:43:51: #2 number of paired peaks: 170 WARNING @ Tue, 02 Aug 2022 14:43:51: Fewer paired peaks (170) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 170 pairs to build model! INFO @ Tue, 02 Aug 2022 14:43:51: start model_add_line... INFO @ Tue, 02 Aug 2022 14:43:51: start X-correlation... INFO @ Tue, 02 Aug 2022 14:43:51: end of X-cor INFO @ Tue, 02 Aug 2022 14:43:51: #2 finished! INFO @ Tue, 02 Aug 2022 14:43:51: #2 predicted fragment length is 97 bps INFO @ Tue, 02 Aug 2022 14:43:51: #2 alternative fragment length(s) may be 97 bps INFO @ Tue, 02 Aug 2022 14:43:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206451/SRX15206451.05_model.r WARNING @ Tue, 02 Aug 2022 14:43:51: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:43:51: #2 You may need to consider one of the other alternative d(s): 97 WARNING @ Tue, 02 Aug 2022 14:43:51: #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 14:43:51: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:43:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:43:53: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:43:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206451/SRX15206451.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:43:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206451/SRX15206451.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:43:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206451/SRX15206451.05_summits.bed INFO @ Tue, 02 Aug 2022 14:43:55: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (193 records, 4 fields): 17 millis CompletedMACS2peakCalling 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 14:44:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206451/SRX15206451.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206451/SRX15206451.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206451/SRX15206451.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206451/SRX15206451.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 14:44:13: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:44:13: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:44:20: 1000000 INFO @ Tue, 02 Aug 2022 14:44:20: #1 tag size is determined as 100 bps INFO @ Tue, 02 Aug 2022 14:44:20: #1 tag size = 100 INFO @ Tue, 02 Aug 2022 14:44:20: #1 total tags in treatment: 1004982 INFO @ Tue, 02 Aug 2022 14:44:20: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:44:20: #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 14:44:20: #1 tags after filtering in treatment: 1004982 INFO @ Tue, 02 Aug 2022 14:44:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:44:20: #1 finished! INFO @ Tue, 02 Aug 2022 14:44:20: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:44:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:44:21: #2 number of paired peaks: 170 WARNING @ Tue, 02 Aug 2022 14:44:21: Fewer paired peaks (170) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 170 pairs to build model! INFO @ Tue, 02 Aug 2022 14:44:21: start model_add_line... INFO @ Tue, 02 Aug 2022 14:44:21: start X-correlation... INFO @ Tue, 02 Aug 2022 14:44:21: end of X-cor INFO @ Tue, 02 Aug 2022 14:44:21: #2 finished! INFO @ Tue, 02 Aug 2022 14:44:21: #2 predicted fragment length is 97 bps INFO @ Tue, 02 Aug 2022 14:44:21: #2 alternative fragment length(s) may be 97 bps INFO @ Tue, 02 Aug 2022 14:44:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206451/SRX15206451.10_model.r WARNING @ Tue, 02 Aug 2022 14:44:21: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:44:21: #2 You may need to consider one of the other alternative d(s): 97 WARNING @ Tue, 02 Aug 2022 14:44:21: #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 14:44:21: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:44:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:44:23: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:44:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206451/SRX15206451.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:44:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206451/SRX15206451.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:44:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206451/SRX15206451.10_summits.bed INFO @ Tue, 02 Aug 2022 14:44:24: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (102 records, 4 fields): 43 millis CompletedMACS2peakCalling 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 14:44:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206451/SRX15206451.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206451/SRX15206451.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206451/SRX15206451.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206451/SRX15206451.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 14:44:43: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:44:43: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:44:51: 1000000 INFO @ Tue, 02 Aug 2022 14:44:51: #1 tag size is determined as 100 bps INFO @ Tue, 02 Aug 2022 14:44:51: #1 tag size = 100 INFO @ Tue, 02 Aug 2022 14:44:51: #1 total tags in treatment: 1004982 INFO @ Tue, 02 Aug 2022 14:44:51: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:44:51: #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 14:44:51: #1 tags after filtering in treatment: 1004982 INFO @ Tue, 02 Aug 2022 14:44:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:44:51: #1 finished! INFO @ Tue, 02 Aug 2022 14:44:51: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:44:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:44:51: #2 number of paired peaks: 170 WARNING @ Tue, 02 Aug 2022 14:44:51: Fewer paired peaks (170) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 170 pairs to build model! INFO @ Tue, 02 Aug 2022 14:44:51: start model_add_line... INFO @ Tue, 02 Aug 2022 14:44:51: start X-correlation... INFO @ Tue, 02 Aug 2022 14:44:51: end of X-cor INFO @ Tue, 02 Aug 2022 14:44:51: #2 finished! INFO @ Tue, 02 Aug 2022 14:44:51: #2 predicted fragment length is 97 bps INFO @ Tue, 02 Aug 2022 14:44:51: #2 alternative fragment length(s) may be 97 bps INFO @ Tue, 02 Aug 2022 14:44:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206451/SRX15206451.20_model.r WARNING @ Tue, 02 Aug 2022 14:44:52: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:44:52: #2 You may need to consider one of the other alternative d(s): 97 WARNING @ Tue, 02 Aug 2022 14:44:52: #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 14:44:52: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:44:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:44:54: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:44:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206451/SRX15206451.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:44:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206451/SRX15206451.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:44:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206451/SRX15206451.20_summits.bed INFO @ Tue, 02 Aug 2022 14:44:55: Done! pass1 - making usageList (4 chroms): 0 millis pass2 - checking and writing primary data (48 records, 4 fields): 11 millis CompletedMACS2peakCalling