Job ID = 16439731 SRX = SRX14894224 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 'SRR18795797'... 2022-08-02T07:02:21 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T07:02:56 prefetch.2.10.7: HTTPS download succeed 2022-08-02T07:02:57 prefetch.2.10.7: 'SRR18795797' is valid 2022-08-02T07:02:57 prefetch.2.10.7: 1) 'SRR18795797' was downloaded successfully 2022-08-02T07:02:57 prefetch.2.10.7: 'SRR18795797' has 0 unresolved dependencies Read 25512212 spots for SRR18795797/SRR18795797.sra Written 25512212 spots for SRR18795797/SRR18795797.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439833 ("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: 00:08:22 25512212 reads; of these: 25512212 (100.00%) were unpaired; of these: 2031457 (7.96%) aligned 0 times 18058677 (70.78%) aligned exactly 1 time 5422078 (21.25%) aligned >1 times 92.04% overall alignment rate Time searching: 00:08:22 Overall time: 00:08:22 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 12 files... [bam_rmdupse_core] 17309996 / 23480755 = 0.7372 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 16:16:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14894224/SRX14894224.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14894224/SRX14894224.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14894224/SRX14894224.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14894224/SRX14894224.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 16:16:56: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:16:56: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:17:02: 1000000 INFO @ Tue, 02 Aug 2022 16:17:09: 2000000 INFO @ Tue, 02 Aug 2022 16:17:15: 3000000 INFO @ Tue, 02 Aug 2022 16:17:21: 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 16:17:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14894224/SRX14894224.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14894224/SRX14894224.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14894224/SRX14894224.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14894224/SRX14894224.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 16:17:25: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:17:25: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:17:27: 5000000 INFO @ Tue, 02 Aug 2022 16:17:32: 1000000 INFO @ Tue, 02 Aug 2022 16:17:33: 6000000 INFO @ Tue, 02 Aug 2022 16:17:34: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 16:17:34: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 16:17:34: #1 total tags in treatment: 6170759 INFO @ Tue, 02 Aug 2022 16:17:34: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:17:34: #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 16:17:34: #1 tags after filtering in treatment: 6170759 INFO @ Tue, 02 Aug 2022 16:17:34: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 16:17:34: #1 finished! INFO @ Tue, 02 Aug 2022 16:17:34: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:17:34: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:17:34: #2 number of paired peaks: 2564 INFO @ Tue, 02 Aug 2022 16:17:34: start model_add_line... INFO @ Tue, 02 Aug 2022 16:17:35: start X-correlation... INFO @ Tue, 02 Aug 2022 16:17:35: end of X-cor INFO @ Tue, 02 Aug 2022 16:17:35: #2 finished! INFO @ Tue, 02 Aug 2022 16:17:35: #2 predicted fragment length is 75 bps INFO @ Tue, 02 Aug 2022 16:17:35: #2 alternative fragment length(s) may be 75,563 bps INFO @ Tue, 02 Aug 2022 16:17:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14894224/SRX14894224.05_model.r WARNING @ Tue, 02 Aug 2022 16:17:35: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 16:17:35: #2 You may need to consider one of the other alternative d(s): 75,563 WARNING @ Tue, 02 Aug 2022 16:17:35: #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 16:17:35: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:17:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:17:38: 2000000 INFO @ Tue, 02 Aug 2022 16:17:45: 3000000 INFO @ Tue, 02 Aug 2022 16:17:50: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:17:52: 4000000 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 16:17:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX14894224/SRX14894224.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX14894224/SRX14894224.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX14894224/SRX14894224.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX14894224/SRX14894224.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 16:17:56: #1 read tag files... INFO @ Tue, 02 Aug 2022 16:17:56: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 16:17:57: 5000000 INFO @ Tue, 02 Aug 2022 16:17:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14894224/SRX14894224.05_peaks.xls INFO @ Tue, 02 Aug 2022 16:17:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14894224/SRX14894224.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:17:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14894224/SRX14894224.05_summits.bed INFO @ Tue, 02 Aug 2022 16:17:58: Done! pass1 - making usageList (15 chroms): 7 millis pass2 - checking and writing primary data (3490 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 16:18:02: 1000000 INFO @ Tue, 02 Aug 2022 16:18:04: 6000000 INFO @ Tue, 02 Aug 2022 16:18:05: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 16:18:05: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 16:18:05: #1 total tags in treatment: 6170759 INFO @ Tue, 02 Aug 2022 16:18:05: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:18:05: #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 16:18:05: #1 tags after filtering in treatment: 6170759 INFO @ Tue, 02 Aug 2022 16:18:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 16:18:05: #1 finished! INFO @ Tue, 02 Aug 2022 16:18:05: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:18:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:18:06: #2 number of paired peaks: 2564 INFO @ Tue, 02 Aug 2022 16:18:06: start model_add_line... INFO @ Tue, 02 Aug 2022 16:18:06: start X-correlation... INFO @ Tue, 02 Aug 2022 16:18:06: end of X-cor INFO @ Tue, 02 Aug 2022 16:18:06: #2 finished! INFO @ Tue, 02 Aug 2022 16:18:06: #2 predicted fragment length is 75 bps INFO @ Tue, 02 Aug 2022 16:18:06: #2 alternative fragment length(s) may be 75,563 bps INFO @ Tue, 02 Aug 2022 16:18:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14894224/SRX14894224.10_model.r WARNING @ Tue, 02 Aug 2022 16:18:06: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 16:18:06: #2 You may need to consider one of the other alternative d(s): 75,563 WARNING @ Tue, 02 Aug 2022 16:18:06: #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 16:18:06: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:18:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 16:18:08: 2000000 INFO @ Tue, 02 Aug 2022 16:18:14: 3000000 INFO @ Tue, 02 Aug 2022 16:18:20: 4000000 INFO @ Tue, 02 Aug 2022 16:18:20: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 16:18:25: 5000000 INFO @ Tue, 02 Aug 2022 16:18:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14894224/SRX14894224.10_peaks.xls INFO @ Tue, 02 Aug 2022 16:18:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14894224/SRX14894224.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:18:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14894224/SRX14894224.10_summits.bed INFO @ Tue, 02 Aug 2022 16:18:29: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1912 records, 4 fields): 70 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 16:18:31: 6000000 INFO @ Tue, 02 Aug 2022 16:18:32: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 16:18:32: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 16:18:32: #1 total tags in treatment: 6170759 INFO @ Tue, 02 Aug 2022 16:18:32: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 16:18:32: #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 16:18:32: #1 tags after filtering in treatment: 6170759 INFO @ Tue, 02 Aug 2022 16:18:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 16:18:32: #1 finished! INFO @ Tue, 02 Aug 2022 16:18:32: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 16:18:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 16:18:32: #2 number of paired peaks: 2564 INFO @ Tue, 02 Aug 2022 16:18:32: start model_add_line... INFO @ Tue, 02 Aug 2022 16:18:32: start X-correlation... INFO @ Tue, 02 Aug 2022 16:18:32: end of X-cor INFO @ Tue, 02 Aug 2022 16:18:32: #2 finished! INFO @ Tue, 02 Aug 2022 16:18:32: #2 predicted fragment length is 75 bps INFO @ Tue, 02 Aug 2022 16:18:32: #2 alternative fragment length(s) may be 75,563 bps INFO @ Tue, 02 Aug 2022 16:18:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX14894224/SRX14894224.20_model.r WARNING @ Tue, 02 Aug 2022 16:18:32: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 16:18:32: #2 You may need to consider one of the other alternative d(s): 75,563 WARNING @ Tue, 02 Aug 2022 16:18:32: #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 16:18:32: #3 Call peaks... INFO @ Tue, 02 Aug 2022 16:18:32: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 16:18:47: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 16:18:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX14894224/SRX14894224.20_peaks.xls INFO @ Tue, 02 Aug 2022 16:18:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX14894224/SRX14894224.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 16:18:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX14894224/SRX14894224.20_summits.bed INFO @ Tue, 02 Aug 2022 16:18:55: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (1010 records, 4 fields): 150 millis CompletedMACS2peakCalling