Job ID = 16439311 SRX = SRX15206489 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T05:52:01 prefetch.2.10.7: 1) Downloading 'SRR19139311'... 2022-08-02T05:52:01 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T05:52:11 prefetch.2.10.7: HTTPS download succeed 2022-08-02T05:52:11 prefetch.2.10.7: 'SRR19139311' is valid 2022-08-02T05:52:11 prefetch.2.10.7: 1) 'SRR19139311' was downloaded successfully 2022-08-02T05:52:11 prefetch.2.10.7: 'SRR19139311' has 0 unresolved dependencies Read 4341705 spots for SRR19139311/SRR19139311.sra Written 4341705 spots for SRR19139311/SRR19139311.sra 2022-08-02T05:52:34 prefetch.2.10.7: 1) Downloading 'SRR19139312'... 2022-08-02T05:52:34 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T05:52:38 prefetch.2.10.7: HTTPS download succeed 2022-08-02T05:52:38 prefetch.2.10.7: 'SRR19139312' is valid 2022-08-02T05:52:38 prefetch.2.10.7: 1) 'SRR19139312' was downloaded successfully 2022-08-02T05:52:38 prefetch.2.10.7: 'SRR19139312' has 0 unresolved dependencies Read 840130 spots for SRR19139312/SRR19139312.sra Written 840130 spots for SRR19139312/SRR19139312.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439380 ("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: 00:06:13 5181835 reads; of these: 5181835 (100.00%) were unpaired; of these: 170725 (3.29%) aligned 0 times 1240584 (23.94%) aligned exactly 1 time 3770526 (72.76%) aligned >1 times 96.71% overall alignment rate Time searching: 00:06:13 Overall time: 00:06:13 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] 1501911 / 5011110 = 0.2997 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 15:01:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206489/SRX15206489.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206489/SRX15206489.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206489/SRX15206489.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206489/SRX15206489.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 15:01:15: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:01:15: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:01:24: 1000000 INFO @ Tue, 02 Aug 2022 15:01:32: 2000000 INFO @ Tue, 02 Aug 2022 15:01:40: 3000000 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 15:01:44: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 15:01:44: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 15:01:44: #1 total tags in treatment: 3509199 INFO @ Tue, 02 Aug 2022 15:01:44: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:01:44: #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 15:01:44: #1 tags after filtering in treatment: 3509199 INFO @ Tue, 02 Aug 2022 15:01:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:01:44: #1 finished! INFO @ Tue, 02 Aug 2022 15:01:44: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:01:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:01:44: #2 number of paired peaks: 5383 INFO @ Tue, 02 Aug 2022 15:01:44: start model_add_line... INFO @ Tue, 02 Aug 2022 15:01:45: start X-correlation... INFO @ Tue, 02 Aug 2022 15:01:45: end of X-cor INFO @ Tue, 02 Aug 2022 15:01:45: #2 finished! INFO @ Tue, 02 Aug 2022 15:01:45: #2 predicted fragment length is 71 bps INFO @ Tue, 02 Aug 2022 15:01:45: #2 alternative fragment length(s) may be 71 bps INFO @ Tue, 02 Aug 2022 15:01:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206489/SRX15206489.05_model.r WARNING @ Tue, 02 Aug 2022 15:01:45: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:01:45: #2 You may need to consider one of the other alternative d(s): 71 WARNING @ Tue, 02 Aug 2022 15:01:45: #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 15:01:45: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:01:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:01:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206489/SRX15206489.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206489/SRX15206489.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206489/SRX15206489.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206489/SRX15206489.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 15:01:45: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:01:45: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:01:55: 1000000 INFO @ Tue, 02 Aug 2022 15:01:56: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:02:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206489/SRX15206489.05_peaks.xls INFO @ Tue, 02 Aug 2022 15:02:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206489/SRX15206489.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:02:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206489/SRX15206489.05_summits.bed INFO @ Tue, 02 Aug 2022 15:02:02: Done! pass1 - making usageList (13 chroms): 5 millis pass2 - checking and writing primary data (8243 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:02:04: 2000000 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 15:02:13: 3000000 INFO @ Tue, 02 Aug 2022 15:02:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206489/SRX15206489.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206489/SRX15206489.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206489/SRX15206489.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206489/SRX15206489.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 15:02:15: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:02:15: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:02:18: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 15:02:18: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 15:02:18: #1 total tags in treatment: 3509199 INFO @ Tue, 02 Aug 2022 15:02:18: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:02:18: #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 15:02:18: #1 tags after filtering in treatment: 3509199 INFO @ Tue, 02 Aug 2022 15:02:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:02:18: #1 finished! INFO @ Tue, 02 Aug 2022 15:02:18: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:02:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:02:19: #2 number of paired peaks: 5383 INFO @ Tue, 02 Aug 2022 15:02:19: start model_add_line... INFO @ Tue, 02 Aug 2022 15:02:19: start X-correlation... INFO @ Tue, 02 Aug 2022 15:02:19: end of X-cor INFO @ Tue, 02 Aug 2022 15:02:19: #2 finished! INFO @ Tue, 02 Aug 2022 15:02:19: #2 predicted fragment length is 71 bps INFO @ Tue, 02 Aug 2022 15:02:19: #2 alternative fragment length(s) may be 71 bps INFO @ Tue, 02 Aug 2022 15:02:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206489/SRX15206489.10_model.r WARNING @ Tue, 02 Aug 2022 15:02:19: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:02:19: #2 You may need to consider one of the other alternative d(s): 71 WARNING @ Tue, 02 Aug 2022 15:02:19: #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 15:02:19: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:02:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:02:25: 1000000 INFO @ Tue, 02 Aug 2022 15:02:30: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:02:35: 2000000 INFO @ Tue, 02 Aug 2022 15:02:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206489/SRX15206489.10_peaks.xls BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 15:02:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206489/SRX15206489.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:02:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206489/SRX15206489.10_summits.bed INFO @ Tue, 02 Aug 2022 15:02:37: Done! pass1 - making usageList (13 chroms): 3 millis pass2 - checking and writing primary data (4919 records, 4 fields): 36 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:02:45: 3000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 15:02:50: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 15:02:50: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 15:02:50: #1 total tags in treatment: 3509199 INFO @ Tue, 02 Aug 2022 15:02:50: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:02:50: #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 15:02:50: #1 tags after filtering in treatment: 3509199 INFO @ Tue, 02 Aug 2022 15:02:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:02:50: #1 finished! INFO @ Tue, 02 Aug 2022 15:02:50: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:02:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:02:51: #2 number of paired peaks: 5383 INFO @ Tue, 02 Aug 2022 15:02:51: start model_add_line... INFO @ Tue, 02 Aug 2022 15:02:51: start X-correlation... INFO @ Tue, 02 Aug 2022 15:02:51: end of X-cor INFO @ Tue, 02 Aug 2022 15:02:51: #2 finished! INFO @ Tue, 02 Aug 2022 15:02:51: #2 predicted fragment length is 71 bps INFO @ Tue, 02 Aug 2022 15:02:51: #2 alternative fragment length(s) may be 71 bps INFO @ Tue, 02 Aug 2022 15:02:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206489/SRX15206489.20_model.r WARNING @ Tue, 02 Aug 2022 15:02:51: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:02:51: #2 You may need to consider one of the other alternative d(s): 71 WARNING @ Tue, 02 Aug 2022 15:02:51: #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 15:02:51: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:02:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:03:02: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:03:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206489/SRX15206489.20_peaks.xls INFO @ Tue, 02 Aug 2022 15:03:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206489/SRX15206489.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:03:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206489/SRX15206489.20_summits.bed INFO @ Tue, 02 Aug 2022 15:03:08: Done! pass1 - making usageList (12 chroms): 3 millis pass2 - checking and writing primary data (881 records, 4 fields): 16 millis CompletedMACS2peakCalling