Job ID = 16439747 SRX = SRX14894236 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T07:04:51 prefetch.2.10.7: 1) Downloading 'SRR18795785'... 2022-08-02T07:04:51 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T07:05:42 prefetch.2.10.7: HTTPS download succeed 2022-08-02T07:05:42 prefetch.2.10.7: 1) 'SRR18795785' was downloaded successfully 2022-08-02T07:05:42 prefetch.2.10.7: 'SRR18795785' has 0 unresolved dependencies Read 34904726 spots for SRR18795785/SRR18795785.sra Written 34904726 spots for SRR18795785/SRR18795785.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439858 ("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: 00:11:25 34904726 reads; of these: 34904726 (100.00%) were unpaired; of these: 3233123 (9.26%) aligned 0 times 22799468 (65.32%) aligned exactly 1 time 8872135 (25.42%) aligned >1 times 90.74% overall alignment rate Time searching: 00:11:25 Overall time: 00:11:25 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_rmdupse_core] 24566812 / 31671603 = 0.7757 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 16:23:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14894236/SRX14894236.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14894236/SRX14894236.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14894236/SRX14894236.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14894236/SRX14894236.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 16:23:48: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:23:48: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:23:53: 1000000 INFO @ Tue, 02 Aug 2022 16:23:59: 2000000 INFO @ Tue, 02 Aug 2022 16:24:04: 3000000 INFO @ Tue, 02 Aug 2022 16:24:09: 4000000 INFO @ Tue, 02 Aug 2022 16:24:15: 5000000 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 16:24:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14894236/SRX14894236.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14894236/SRX14894236.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14894236/SRX14894236.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14894236/SRX14894236.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 16:24:17: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:24:17: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:24:20: 6000000 INFO @ Tue, 02 Aug 2022 16:24:22: 1000000 INFO @ Tue, 02 Aug 2022 16:24:25: 7000000 INFO @ Tue, 02 Aug 2022 16:24:26: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 16:24:26: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 16:24:26: #1 total tags in treatment: 7104791 INFO @ Tue, 02 Aug 2022 16:24:26: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:24:26: #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 16:24:26: #1 tags after filtering in treatment: 7104791 INFO @ Tue, 02 Aug 2022 16:24:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 16:24:26: #1 finished! INFO @ Tue, 02 Aug 2022 16:24:26: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:24:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:24:27: #2 number of paired peaks: 2643 INFO @ Tue, 02 Aug 2022 16:24:27: start model_add_line... INFO @ Tue, 02 Aug 2022 16:24:27: start X-correlation... INFO @ Tue, 02 Aug 2022 16:24:27: end of X-cor INFO @ Tue, 02 Aug 2022 16:24:27: #2 finished! INFO @ Tue, 02 Aug 2022 16:24:27: #2 predicted fragment length is 84 bps INFO @ Tue, 02 Aug 2022 16:24:27: #2 alternative fragment length(s) may be 84 bps INFO @ Tue, 02 Aug 2022 16:24:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14894236/SRX14894236.05_model.r WARNING @ Tue, 02 Aug 2022 16:24:27: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 16:24:27: #2 You may need to consider one of the other alternative d(s): 84 WARNING @ Tue, 02 Aug 2022 16:24:27: #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 16:24:27: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:24:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:24:28: 2000000 INFO @ Tue, 02 Aug 2022 16:24:33: 3000000 INFO @ Tue, 02 Aug 2022 16:24:38: 4000000 INFO @ Tue, 02 Aug 2022 16:24:43: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:24:43: 5000000 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 16:24:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14894236/SRX14894236.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14894236/SRX14894236.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14894236/SRX14894236.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14894236/SRX14894236.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 16:24:47: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:24:47: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:24:48: 6000000 INFO @ Tue, 02 Aug 2022 16:24:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14894236/SRX14894236.05_peaks.xls INFO @ Tue, 02 Aug 2022 16:24:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14894236/SRX14894236.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:24:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14894236/SRX14894236.05_summits.bed INFO @ Tue, 02 Aug 2022 16:24:51: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4581 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 16:24:53: 1000000 INFO @ Tue, 02 Aug 2022 16:24:53: 7000000 INFO @ Tue, 02 Aug 2022 16:24:53: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 16:24:53: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 16:24:53: #1 total tags in treatment: 7104791 INFO @ Tue, 02 Aug 2022 16:24:53: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:24:53: #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 16:24:54: #1 tags after filtering in treatment: 7104791 INFO @ Tue, 02 Aug 2022 16:24:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 16:24:54: #1 finished! INFO @ Tue, 02 Aug 2022 16:24:54: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:24:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:24:54: #2 number of paired peaks: 2643 INFO @ Tue, 02 Aug 2022 16:24:54: start model_add_line... INFO @ Tue, 02 Aug 2022 16:24:54: start X-correlation... INFO @ Tue, 02 Aug 2022 16:24:54: end of X-cor INFO @ Tue, 02 Aug 2022 16:24:54: #2 finished! INFO @ Tue, 02 Aug 2022 16:24:54: #2 predicted fragment length is 84 bps INFO @ Tue, 02 Aug 2022 16:24:54: #2 alternative fragment length(s) may be 84 bps INFO @ Tue, 02 Aug 2022 16:24:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14894236/SRX14894236.10_model.r WARNING @ Tue, 02 Aug 2022 16:24:54: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 16:24:54: #2 You may need to consider one of the other alternative d(s): 84 WARNING @ Tue, 02 Aug 2022 16:24:54: #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 16:24:54: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:24:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:24:58: 2000000 INFO @ Tue, 02 Aug 2022 16:25:03: 3000000 INFO @ Tue, 02 Aug 2022 16:25:08: 4000000 INFO @ Tue, 02 Aug 2022 16:25:10: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:25:14: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 16:25:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14894236/SRX14894236.10_peaks.xls INFO @ Tue, 02 Aug 2022 16:25:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14894236/SRX14894236.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:25:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14894236/SRX14894236.10_summits.bed INFO @ Tue, 02 Aug 2022 16:25:18: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2298 records, 4 fields): 61 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 16:25:19: 6000000 INFO @ Tue, 02 Aug 2022 16:25:24: 7000000 INFO @ Tue, 02 Aug 2022 16:25:24: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 16:25:24: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 16:25:24: #1 total tags in treatment: 7104791 INFO @ Tue, 02 Aug 2022 16:25:24: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:25:24: #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 16:25:24: #1 tags after filtering in treatment: 7104791 INFO @ Tue, 02 Aug 2022 16:25:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 16:25:24: #1 finished! INFO @ Tue, 02 Aug 2022 16:25:24: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:25:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:25:25: #2 number of paired peaks: 2643 INFO @ Tue, 02 Aug 2022 16:25:25: start model_add_line... INFO @ Tue, 02 Aug 2022 16:25:25: start X-correlation... INFO @ Tue, 02 Aug 2022 16:25:25: end of X-cor INFO @ Tue, 02 Aug 2022 16:25:25: #2 finished! INFO @ Tue, 02 Aug 2022 16:25:25: #2 predicted fragment length is 84 bps INFO @ Tue, 02 Aug 2022 16:25:25: #2 alternative fragment length(s) may be 84 bps INFO @ Tue, 02 Aug 2022 16:25:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14894236/SRX14894236.20_model.r WARNING @ Tue, 02 Aug 2022 16:25:25: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 16:25:25: #2 You may need to consider one of the other alternative d(s): 84 WARNING @ Tue, 02 Aug 2022 16:25:25: #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 16:25:25: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:25:25: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 16:25:41: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:25:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14894236/SRX14894236.20_peaks.xls INFO @ Tue, 02 Aug 2022 16:25:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14894236/SRX14894236.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:25:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14894236/SRX14894236.20_summits.bed INFO @ Tue, 02 Aug 2022 16:25:51: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1074 records, 4 fields): 22 millis CompletedMACS2peakCalling