Job ID = 16439732 SRX = SRX14894225 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T07:02:21 prefetch.2.10.7: 1) Downloading 'SRR18795796'... 2022-08-02T07:02:21 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T07:02:54 prefetch.2.10.7: HTTPS download succeed 2022-08-02T07:02:54 prefetch.2.10.7: 'SRR18795796' is valid 2022-08-02T07:02:54 prefetch.2.10.7: 1) 'SRR18795796' was downloaded successfully 2022-08-02T07:02:54 prefetch.2.10.7: 'SRR18795796' has 0 unresolved dependencies Read 16073310 spots for SRR18795796/SRR18795796.sra Written 16073310 spots for SRR18795796/SRR18795796.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439816 ("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: 00:05:07 16073310 reads; of these: 16073310 (100.00%) were unpaired; of these: 1454202 (9.05%) aligned 0 times 10950963 (68.13%) aligned exactly 1 time 3668145 (22.82%) aligned >1 times 90.95% overall alignment rate Time searching: 00:05:07 Overall time: 00:05:07 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_rmdupse_core] 9859897 / 14619108 = 0.6745 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 16:12:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14894225/SRX14894225.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14894225/SRX14894225.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14894225/SRX14894225.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14894225/SRX14894225.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 16:12:36: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:12:36: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:12:44: 1000000 INFO @ Tue, 02 Aug 2022 16:12:51: 2000000 INFO @ Tue, 02 Aug 2022 16:12:58: 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 16:13:05: 4000000 INFO @ Tue, 02 Aug 2022 16:13:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14894225/SRX14894225.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14894225/SRX14894225.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14894225/SRX14894225.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14894225/SRX14894225.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 16:13:05: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:13:05: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:13:10: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 16:13:10: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 16:13:10: #1 total tags in treatment: 4759211 INFO @ Tue, 02 Aug 2022 16:13:10: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:13:10: #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 16:13:10: #1 tags after filtering in treatment: 4759211 INFO @ Tue, 02 Aug 2022 16:13:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 16:13:10: #1 finished! INFO @ Tue, 02 Aug 2022 16:13:10: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:13:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:13:10: #2 number of paired peaks: 2238 INFO @ Tue, 02 Aug 2022 16:13:10: start model_add_line... INFO @ Tue, 02 Aug 2022 16:13:10: start X-correlation... INFO @ Tue, 02 Aug 2022 16:13:11: end of X-cor INFO @ Tue, 02 Aug 2022 16:13:11: #2 finished! INFO @ Tue, 02 Aug 2022 16:13:11: #2 predicted fragment length is 63 bps INFO @ Tue, 02 Aug 2022 16:13:11: #2 alternative fragment length(s) may be 63 bps INFO @ Tue, 02 Aug 2022 16:13:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14894225/SRX14894225.05_model.r WARNING @ Tue, 02 Aug 2022 16:13:11: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 16:13:11: #2 You may need to consider one of the other alternative d(s): 63 WARNING @ Tue, 02 Aug 2022 16:13:11: #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 16:13:11: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:13:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:13:14: 1000000 INFO @ Tue, 02 Aug 2022 16:13:20: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:13:23: 2000000 INFO @ Tue, 02 Aug 2022 16:13:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14894225/SRX14894225.05_peaks.xls INFO @ Tue, 02 Aug 2022 16:13:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14894225/SRX14894225.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:13:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14894225/SRX14894225.05_summits.bed INFO @ Tue, 02 Aug 2022 16:13:26: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2432 records, 4 fields): 60 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 16:13:31: 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 16:13:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14894225/SRX14894225.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14894225/SRX14894225.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14894225/SRX14894225.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14894225/SRX14894225.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 16:13:35: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:13:35: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:13:40: 4000000 INFO @ Tue, 02 Aug 2022 16:13:42: 1000000 INFO @ Tue, 02 Aug 2022 16:13:46: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 16:13:46: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 16:13:46: #1 total tags in treatment: 4759211 INFO @ Tue, 02 Aug 2022 16:13:46: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:13:46: #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 16:13:47: #1 tags after filtering in treatment: 4759211 INFO @ Tue, 02 Aug 2022 16:13:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 16:13:47: #1 finished! INFO @ Tue, 02 Aug 2022 16:13:47: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:13:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:13:47: #2 number of paired peaks: 2238 INFO @ Tue, 02 Aug 2022 16:13:47: start model_add_line... INFO @ Tue, 02 Aug 2022 16:13:47: start X-correlation... INFO @ Tue, 02 Aug 2022 16:13:47: end of X-cor INFO @ Tue, 02 Aug 2022 16:13:47: #2 finished! INFO @ Tue, 02 Aug 2022 16:13:47: #2 predicted fragment length is 63 bps INFO @ Tue, 02 Aug 2022 16:13:47: #2 alternative fragment length(s) may be 63 bps INFO @ Tue, 02 Aug 2022 16:13:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14894225/SRX14894225.10_model.r WARNING @ Tue, 02 Aug 2022 16:13:47: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 16:13:47: #2 You may need to consider one of the other alternative d(s): 63 WARNING @ Tue, 02 Aug 2022 16:13:47: #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 16:13:47: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:13:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:13:50: 2000000 INFO @ Tue, 02 Aug 2022 16:13:56: 3000000 INFO @ Tue, 02 Aug 2022 16:13:57: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:14:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14894225/SRX14894225.10_peaks.xls INFO @ Tue, 02 Aug 2022 16:14:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14894225/SRX14894225.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:14:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14894225/SRX14894225.10_summits.bed INFO @ Tue, 02 Aug 2022 16:14:02: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1290 records, 4 fields): 37 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 16:14:03: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 16:14:08: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 16:14:08: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 16:14:08: #1 total tags in treatment: 4759211 INFO @ Tue, 02 Aug 2022 16:14:08: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:14:08: #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 16:14:08: #1 tags after filtering in treatment: 4759211 INFO @ Tue, 02 Aug 2022 16:14:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 16:14:08: #1 finished! INFO @ Tue, 02 Aug 2022 16:14:08: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:14:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:14:08: #2 number of paired peaks: 2238 INFO @ Tue, 02 Aug 2022 16:14:08: start model_add_line... INFO @ Tue, 02 Aug 2022 16:14:09: start X-correlation... INFO @ Tue, 02 Aug 2022 16:14:09: end of X-cor INFO @ Tue, 02 Aug 2022 16:14:09: #2 finished! INFO @ Tue, 02 Aug 2022 16:14:09: #2 predicted fragment length is 63 bps INFO @ Tue, 02 Aug 2022 16:14:09: #2 alternative fragment length(s) may be 63 bps INFO @ Tue, 02 Aug 2022 16:14:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14894225/SRX14894225.20_model.r WARNING @ Tue, 02 Aug 2022 16:14:09: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 16:14:09: #2 You may need to consider one of the other alternative d(s): 63 WARNING @ Tue, 02 Aug 2022 16:14:09: #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 16:14:09: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:14:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:14:18: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 16:14:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14894225/SRX14894225.20_peaks.xls INFO @ Tue, 02 Aug 2022 16:14:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14894225/SRX14894225.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:14:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14894225/SRX14894225.20_summits.bed INFO @ Tue, 02 Aug 2022 16:14:23: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (563 records, 4 fields): 17 millis CompletedMACS2peakCalling