Job ID = 16439022 SRX = SRX15206448 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T05:25:51 prefetch.2.10.7: 1) Downloading 'SRR19139360'... 2022-08-02T05:25:51 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T05:26:13 prefetch.2.10.7: HTTPS download succeed 2022-08-02T05:26:14 prefetch.2.10.7: 'SRR19139360' is valid 2022-08-02T05:26:14 prefetch.2.10.7: 1) 'SRR19139360' was downloaded successfully 2022-08-02T05:26:14 prefetch.2.10.7: 'SRR19139360' has 0 unresolved dependencies Read 10661341 spots for SRR19139360/SRR19139360.sra Written 10661341 spots for SRR19139360/SRR19139360.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439163 ("srTdm6") has been submitted Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:10:11 10661341 reads; of these: 10661341 (100.00%) were unpaired; of these: 298657 (2.80%) aligned 0 times 3169575 (29.73%) aligned exactly 1 time 7193109 (67.47%) aligned >1 times 97.20% overall alignment rate Time searching: 00:10:12 Overall time: 00:10:12 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] 3105797 / 10362684 = 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 14:41:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206448/SRX15206448.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206448/SRX15206448.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206448/SRX15206448.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206448/SRX15206448.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 14:41:14: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:41:14: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:41:26: 1000000 INFO @ Tue, 02 Aug 2022 14:41:37: 2000000 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 14:41:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206448/SRX15206448.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206448/SRX15206448.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206448/SRX15206448.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206448/SRX15206448.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 14:41:44: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:41:44: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:41:49: 3000000 INFO @ Tue, 02 Aug 2022 14:41:54: 1000000 INFO @ Tue, 02 Aug 2022 14:42:01: 4000000 INFO @ Tue, 02 Aug 2022 14:42:04: 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 14:42:12: 5000000 INFO @ Tue, 02 Aug 2022 14:42:13: 3000000 INFO @ Tue, 02 Aug 2022 14:42:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206448/SRX15206448.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206448/SRX15206448.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206448/SRX15206448.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206448/SRX15206448.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 14:42:14: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:42:14: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:42:24: 4000000 INFO @ Tue, 02 Aug 2022 14:42:25: 6000000 INFO @ Tue, 02 Aug 2022 14:42:25: 1000000 INFO @ Tue, 02 Aug 2022 14:42:36: 5000000 INFO @ Tue, 02 Aug 2022 14:42:37: 2000000 INFO @ Tue, 02 Aug 2022 14:42:38: 7000000 INFO @ Tue, 02 Aug 2022 14:42:41: #1 tag size is determined as 100 bps INFO @ Tue, 02 Aug 2022 14:42:41: #1 tag size = 100 INFO @ Tue, 02 Aug 2022 14:42:41: #1 total tags in treatment: 7256887 INFO @ Tue, 02 Aug 2022 14:42:41: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:42:41: #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 14:42:41: #1 tags after filtering in treatment: 7256887 INFO @ Tue, 02 Aug 2022 14:42:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:42:41: #1 finished! INFO @ Tue, 02 Aug 2022 14:42:41: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:42:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:42:43: #2 number of paired peaks: 6144 INFO @ Tue, 02 Aug 2022 14:42:43: start model_add_line... INFO @ Tue, 02 Aug 2022 14:42:43: start X-correlation... INFO @ Tue, 02 Aug 2022 14:42:43: end of X-cor INFO @ Tue, 02 Aug 2022 14:42:43: #2 finished! INFO @ Tue, 02 Aug 2022 14:42:43: #2 predicted fragment length is 171 bps INFO @ Tue, 02 Aug 2022 14:42:43: #2 alternative fragment length(s) may be 171 bps INFO @ Tue, 02 Aug 2022 14:42:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206448/SRX15206448.05_model.r WARNING @ Tue, 02 Aug 2022 14:42:43: #2 Since the d (171) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:42:43: #2 You may need to consider one of the other alternative d(s): 171 WARNING @ Tue, 02 Aug 2022 14:42:43: #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 14:42:43: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:42:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:42:47: 6000000 INFO @ Tue, 02 Aug 2022 14:42:48: 3000000 INFO @ Tue, 02 Aug 2022 14:42:58: 7000000 INFO @ Tue, 02 Aug 2022 14:43:00: 4000000 INFO @ Tue, 02 Aug 2022 14:43:01: #1 tag size is determined as 100 bps INFO @ Tue, 02 Aug 2022 14:43:01: #1 tag size = 100 INFO @ Tue, 02 Aug 2022 14:43:01: #1 total tags in treatment: 7256887 INFO @ Tue, 02 Aug 2022 14:43:01: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:43:01: #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 14:43:01: #1 tags after filtering in treatment: 7256887 INFO @ Tue, 02 Aug 2022 14:43:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:43:01: #1 finished! INFO @ Tue, 02 Aug 2022 14:43:01: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:43:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:43:02: #2 number of paired peaks: 6144 INFO @ Tue, 02 Aug 2022 14:43:02: start model_add_line... INFO @ Tue, 02 Aug 2022 14:43:02: start X-correlation... INFO @ Tue, 02 Aug 2022 14:43:02: end of X-cor INFO @ Tue, 02 Aug 2022 14:43:02: #2 finished! INFO @ Tue, 02 Aug 2022 14:43:02: #2 predicted fragment length is 171 bps INFO @ Tue, 02 Aug 2022 14:43:02: #2 alternative fragment length(s) may be 171 bps INFO @ Tue, 02 Aug 2022 14:43:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206448/SRX15206448.10_model.r WARNING @ Tue, 02 Aug 2022 14:43:02: #2 Since the d (171) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:43:02: #2 You may need to consider one of the other alternative d(s): 171 WARNING @ Tue, 02 Aug 2022 14:43:02: #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 14:43:02: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:43:02: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:43:09: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:43:11: 5000000 INFO @ Tue, 02 Aug 2022 14:43:21: 6000000 INFO @ Tue, 02 Aug 2022 14:43:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206448/SRX15206448.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:43:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206448/SRX15206448.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:43:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206448/SRX15206448.05_summits.bed INFO @ Tue, 02 Aug 2022 14:43:23: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (11556 records, 4 fields): 46 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:43:32: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:43:33: 7000000 INFO @ Tue, 02 Aug 2022 14:43:36: #1 tag size is determined as 100 bps INFO @ Tue, 02 Aug 2022 14:43:36: #1 tag size = 100 INFO @ Tue, 02 Aug 2022 14:43:36: #1 total tags in treatment: 7256887 INFO @ Tue, 02 Aug 2022 14:43:36: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:43:36: #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 14:43:36: #1 tags after filtering in treatment: 7256887 INFO @ Tue, 02 Aug 2022 14:43:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:43:36: #1 finished! INFO @ Tue, 02 Aug 2022 14:43:36: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:43:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:43:37: #2 number of paired peaks: 6144 INFO @ Tue, 02 Aug 2022 14:43:37: start model_add_line... INFO @ Tue, 02 Aug 2022 14:43:37: start X-correlation... INFO @ Tue, 02 Aug 2022 14:43:37: end of X-cor INFO @ Tue, 02 Aug 2022 14:43:37: #2 finished! INFO @ Tue, 02 Aug 2022 14:43:37: #2 predicted fragment length is 171 bps INFO @ Tue, 02 Aug 2022 14:43:37: #2 alternative fragment length(s) may be 171 bps INFO @ Tue, 02 Aug 2022 14:43:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206448/SRX15206448.20_model.r WARNING @ Tue, 02 Aug 2022 14:43:37: #2 Since the d (171) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:43:37: #2 You may need to consider one of the other alternative d(s): 171 WARNING @ Tue, 02 Aug 2022 14:43:37: #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 14:43:37: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:43:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:43:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206448/SRX15206448.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:43:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206448/SRX15206448.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:43:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206448/SRX15206448.10_summits.bed INFO @ Tue, 02 Aug 2022 14:43:47: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (7389 records, 4 fields): 38 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:44:05: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:44:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206448/SRX15206448.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:44:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206448/SRX15206448.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:44:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206448/SRX15206448.20_summits.bed INFO @ Tue, 02 Aug 2022 14:44:20: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (3871 records, 4 fields): 38 millis CompletedMACS2peakCalling