Job ID = 16438972 SRX = SRX15206529 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T05:17:54 prefetch.2.10.7: 1) Downloading 'SRR19139263'... 2022-08-02T05:17:54 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T05:18:36 prefetch.2.10.7: HTTPS download succeed 2022-08-02T05:18:36 prefetch.2.10.7: 1) 'SRR19139263' was downloaded successfully 2022-08-02T05:18:36 prefetch.2.10.7: 'SRR19139263' has 0 unresolved dependencies Read 11749126 spots for SRR19139263/SRR19139263.sra Written 11749126 spots for SRR19139263/SRR19139263.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439146 ("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: 00:09:01 11749126 reads; of these: 11749126 (100.00%) were unpaired; of these: 1080912 (9.20%) aligned 0 times 9107504 (77.52%) aligned exactly 1 time 1560710 (13.28%) aligned >1 times 90.80% overall alignment rate Time searching: 00:09:01 Overall time: 00:09:01 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] 3120099 / 10668214 = 0.2925 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 14:36:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206529/SRX15206529.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206529/SRX15206529.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206529/SRX15206529.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206529/SRX15206529.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 14:36:25: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:36:25: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:36:33: 1000000 INFO @ Tue, 02 Aug 2022 14:36:41: 2000000 INFO @ Tue, 02 Aug 2022 14:36:50: 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 14:36:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206529/SRX15206529.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206529/SRX15206529.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206529/SRX15206529.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206529/SRX15206529.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 14:36:54: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:36:54: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:36:59: 4000000 INFO @ Tue, 02 Aug 2022 14:37:02: 1000000 INFO @ Tue, 02 Aug 2022 14:37:07: 5000000 INFO @ Tue, 02 Aug 2022 14:37:11: 2000000 INFO @ Tue, 02 Aug 2022 14:37:16: 6000000 INFO @ Tue, 02 Aug 2022 14:37:19: 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 14:37:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206529/SRX15206529.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206529/SRX15206529.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206529/SRX15206529.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206529/SRX15206529.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 14:37:24: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:37:24: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:37:25: 7000000 INFO @ Tue, 02 Aug 2022 14:37:28: 4000000 INFO @ Tue, 02 Aug 2022 14:37:30: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 14:37:30: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 14:37:30: #1 total tags in treatment: 7548115 INFO @ Tue, 02 Aug 2022 14:37:30: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:37:30: #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 14:37:30: #1 tags after filtering in treatment: 7548115 INFO @ Tue, 02 Aug 2022 14:37:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:37:30: #1 finished! INFO @ Tue, 02 Aug 2022 14:37:30: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:37:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:37:31: #2 number of paired peaks: 117 WARNING @ Tue, 02 Aug 2022 14:37:31: Fewer paired peaks (117) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 117 pairs to build model! INFO @ Tue, 02 Aug 2022 14:37:31: start model_add_line... INFO @ Tue, 02 Aug 2022 14:37:31: start X-correlation... INFO @ Tue, 02 Aug 2022 14:37:31: end of X-cor INFO @ Tue, 02 Aug 2022 14:37:31: #2 finished! INFO @ Tue, 02 Aug 2022 14:37:31: #2 predicted fragment length is 171 bps INFO @ Tue, 02 Aug 2022 14:37:31: #2 alternative fragment length(s) may be 4,156,162,171 bps INFO @ Tue, 02 Aug 2022 14:37:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206529/SRX15206529.05_model.r WARNING @ Tue, 02 Aug 2022 14:37:31: #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 14:37:31: #2 You may need to consider one of the other alternative d(s): 4,156,162,171 WARNING @ Tue, 02 Aug 2022 14:37:31: #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 14:37:31: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:37:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:37:33: 1000000 INFO @ Tue, 02 Aug 2022 14:37:36: 5000000 INFO @ Tue, 02 Aug 2022 14:37:41: 2000000 INFO @ Tue, 02 Aug 2022 14:37:44: 6000000 INFO @ Tue, 02 Aug 2022 14:37:45: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:37:50: 3000000 INFO @ Tue, 02 Aug 2022 14:37:53: 7000000 INFO @ Tue, 02 Aug 2022 14:37:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206529/SRX15206529.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:37:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206529/SRX15206529.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:37:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206529/SRX15206529.05_summits.bed INFO @ Tue, 02 Aug 2022 14:37:53: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (313 records, 4 fields): 51 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:37:57: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 14:37:57: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 14:37:57: #1 total tags in treatment: 7548115 INFO @ Tue, 02 Aug 2022 14:37:57: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:37:57: #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 14:37:57: #1 tags after filtering in treatment: 7548115 INFO @ Tue, 02 Aug 2022 14:37:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:37:57: #1 finished! INFO @ Tue, 02 Aug 2022 14:37:57: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:37:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:37:58: #2 number of paired peaks: 117 WARNING @ Tue, 02 Aug 2022 14:37:58: Fewer paired peaks (117) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 117 pairs to build model! INFO @ Tue, 02 Aug 2022 14:37:58: start model_add_line... INFO @ Tue, 02 Aug 2022 14:37:58: start X-correlation... INFO @ Tue, 02 Aug 2022 14:37:58: end of X-cor INFO @ Tue, 02 Aug 2022 14:37:58: #2 finished! INFO @ Tue, 02 Aug 2022 14:37:58: #2 predicted fragment length is 171 bps INFO @ Tue, 02 Aug 2022 14:37:58: #2 alternative fragment length(s) may be 4,156,162,171 bps INFO @ Tue, 02 Aug 2022 14:37:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206529/SRX15206529.10_model.r WARNING @ Tue, 02 Aug 2022 14:37:58: #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 14:37:58: #2 You may need to consider one of the other alternative d(s): 4,156,162,171 WARNING @ Tue, 02 Aug 2022 14:37:58: #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 14:37:58: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:37:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:37:59: 4000000 INFO @ Tue, 02 Aug 2022 14:38:07: 5000000 INFO @ Tue, 02 Aug 2022 14:38:12: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:38:15: 6000000 INFO @ Tue, 02 Aug 2022 14:38:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206529/SRX15206529.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:38:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206529/SRX15206529.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:38:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206529/SRX15206529.10_summits.bed INFO @ Tue, 02 Aug 2022 14:38:20: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (137 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:38:24: 7000000 INFO @ Tue, 02 Aug 2022 14:38:28: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 14:38:28: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 14:38:28: #1 total tags in treatment: 7548115 INFO @ Tue, 02 Aug 2022 14:38:28: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:38:28: #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 14:38:29: #1 tags after filtering in treatment: 7548115 INFO @ Tue, 02 Aug 2022 14:38:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:38:29: #1 finished! INFO @ Tue, 02 Aug 2022 14:38:29: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:38:29: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:38:29: #2 number of paired peaks: 117 WARNING @ Tue, 02 Aug 2022 14:38:29: Fewer paired peaks (117) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 117 pairs to build model! INFO @ Tue, 02 Aug 2022 14:38:29: start model_add_line... INFO @ Tue, 02 Aug 2022 14:38:29: start X-correlation... INFO @ Tue, 02 Aug 2022 14:38:29: end of X-cor INFO @ Tue, 02 Aug 2022 14:38:29: #2 finished! INFO @ Tue, 02 Aug 2022 14:38:29: #2 predicted fragment length is 171 bps INFO @ Tue, 02 Aug 2022 14:38:29: #2 alternative fragment length(s) may be 4,156,162,171 bps INFO @ Tue, 02 Aug 2022 14:38:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206529/SRX15206529.20_model.r WARNING @ Tue, 02 Aug 2022 14:38:29: #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 14:38:29: #2 You may need to consider one of the other alternative d(s): 4,156,162,171 WARNING @ Tue, 02 Aug 2022 14:38:29: #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 14:38:29: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:38:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:38:44: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:38:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206529/SRX15206529.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:38:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206529/SRX15206529.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:38:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206529/SRX15206529.20_summits.bed INFO @ Tue, 02 Aug 2022 14:38:51: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (47 records, 4 fields): 14 millis CompletedMACS2peakCalling BigWig に変換しました。