Job ID = 16439313 SRX = SRX15206491 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T05:52:05 prefetch.2.10.7: 1) Downloading 'SRR19139307'... 2022-08-02T05:52:05 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T05:52:33 prefetch.2.10.7: HTTPS download succeed 2022-08-02T05:52:34 prefetch.2.10.7: 'SRR19139307' is valid 2022-08-02T05:52:34 prefetch.2.10.7: 1) 'SRR19139307' was downloaded successfully 2022-08-02T05:52:34 prefetch.2.10.7: 'SRR19139307' has 0 unresolved dependencies Read 15459548 spots for SRR19139307/SRR19139307.sra Written 15459548 spots for SRR19139307/SRR19139307.sra 2022-08-02T05:53:53 prefetch.2.10.7: 1) Downloading 'SRR19139308'... 2022-08-02T05:53:53 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T05:54:02 prefetch.2.10.7: HTTPS download succeed 2022-08-02T05:54:02 prefetch.2.10.7: 'SRR19139308' is valid 2022-08-02T05:54:02 prefetch.2.10.7: 1) 'SRR19139308' was downloaded successfully 2022-08-02T05:54:02 prefetch.2.10.7: 'SRR19139308' has 0 unresolved dependencies Read 3121191 spots for SRR19139308/SRR19139308.sra Written 3121191 spots for SRR19139308/SRR19139308.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439439 ("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: 00:13:45 18580739 reads; of these: 18580739 (100.00%) were unpaired; of these: 258445 (1.39%) aligned 0 times 6651410 (35.80%) aligned exactly 1 time 11670884 (62.81%) aligned >1 times 98.61% overall alignment rate Time searching: 00:13:45 Overall time: 00:13:45 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] 3648526 / 18322294 = 0.1991 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 15:14:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206491/SRX15206491.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206491/SRX15206491.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206491/SRX15206491.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206491/SRX15206491.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 15:14:35: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:14:35: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:14:45: 1000000 INFO @ Tue, 02 Aug 2022 15:14:55: 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 15:15:04: 3000000 INFO @ Tue, 02 Aug 2022 15:15:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206491/SRX15206491.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206491/SRX15206491.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206491/SRX15206491.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206491/SRX15206491.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 15:15:05: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:15:05: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:15:13: 4000000 INFO @ Tue, 02 Aug 2022 15:15:16: 1000000 INFO @ Tue, 02 Aug 2022 15:15:23: 5000000 INFO @ Tue, 02 Aug 2022 15:15:26: 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 15:15:32: 6000000 INFO @ Tue, 02 Aug 2022 15:15:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206491/SRX15206491.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206491/SRX15206491.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206491/SRX15206491.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206491/SRX15206491.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 15:15:35: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:15:35: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:15:36: 3000000 INFO @ Tue, 02 Aug 2022 15:15:42: 7000000 INFO @ Tue, 02 Aug 2022 15:15:45: 1000000 INFO @ Tue, 02 Aug 2022 15:15:46: 4000000 INFO @ Tue, 02 Aug 2022 15:15:51: 8000000 INFO @ Tue, 02 Aug 2022 15:15:56: 2000000 INFO @ Tue, 02 Aug 2022 15:15:58: 5000000 INFO @ Tue, 02 Aug 2022 15:16:01: 9000000 INFO @ Tue, 02 Aug 2022 15:16:06: 3000000 INFO @ Tue, 02 Aug 2022 15:16:08: 6000000 INFO @ Tue, 02 Aug 2022 15:16:09: 10000000 INFO @ Tue, 02 Aug 2022 15:16:17: 4000000 INFO @ Tue, 02 Aug 2022 15:16:18: 7000000 INFO @ Tue, 02 Aug 2022 15:16:21: 11000000 INFO @ Tue, 02 Aug 2022 15:16:27: 5000000 INFO @ Tue, 02 Aug 2022 15:16:29: 8000000 INFO @ Tue, 02 Aug 2022 15:16:34: 12000000 INFO @ Tue, 02 Aug 2022 15:16:37: 6000000 INFO @ Tue, 02 Aug 2022 15:16:39: 9000000 INFO @ Tue, 02 Aug 2022 15:16:47: 13000000 INFO @ Tue, 02 Aug 2022 15:16:48: 7000000 INFO @ Tue, 02 Aug 2022 15:16:48: 10000000 INFO @ Tue, 02 Aug 2022 15:16:58: 8000000 INFO @ Tue, 02 Aug 2022 15:16:58: 11000000 INFO @ Tue, 02 Aug 2022 15:17:00: 14000000 INFO @ Tue, 02 Aug 2022 15:17:08: 9000000 INFO @ Tue, 02 Aug 2022 15:17:08: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 15:17:08: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 15:17:08: #1 total tags in treatment: 14673768 INFO @ Tue, 02 Aug 2022 15:17:08: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:17:08: #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 15:17:09: #1 tags after filtering in treatment: 14673768 INFO @ Tue, 02 Aug 2022 15:17:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:17:09: #1 finished! INFO @ Tue, 02 Aug 2022 15:17:09: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:17:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:17:09: 12000000 INFO @ Tue, 02 Aug 2022 15:17:11: #2 number of paired peaks: 3858 INFO @ Tue, 02 Aug 2022 15:17:11: start model_add_line... INFO @ Tue, 02 Aug 2022 15:17:11: start X-correlation... INFO @ Tue, 02 Aug 2022 15:17:11: end of X-cor INFO @ Tue, 02 Aug 2022 15:17:11: #2 finished! INFO @ Tue, 02 Aug 2022 15:17:11: #2 predicted fragment length is 140 bps INFO @ Tue, 02 Aug 2022 15:17:11: #2 alternative fragment length(s) may be 4,140 bps INFO @ Tue, 02 Aug 2022 15:17:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206491/SRX15206491.05_model.r WARNING @ Tue, 02 Aug 2022 15:17:11: #2 Since the d (140) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:17:11: #2 You may need to consider one of the other alternative d(s): 4,140 WARNING @ Tue, 02 Aug 2022 15:17:11: #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 15:17:11: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:17:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:17:18: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 15:17:19: 13000000 INFO @ Tue, 02 Aug 2022 15:17:27: 11000000 INFO @ Tue, 02 Aug 2022 15:17:28: 14000000 INFO @ Tue, 02 Aug 2022 15:17:35: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 15:17:35: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 15:17:35: #1 total tags in treatment: 14673768 INFO @ Tue, 02 Aug 2022 15:17:35: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:17:35: #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 15:17:35: #1 tags after filtering in treatment: 14673768 INFO @ Tue, 02 Aug 2022 15:17:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:17:35: #1 finished! INFO @ Tue, 02 Aug 2022 15:17:35: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:17:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:17:36: 12000000 INFO @ Tue, 02 Aug 2022 15:17:37: #2 number of paired peaks: 3858 INFO @ Tue, 02 Aug 2022 15:17:37: start model_add_line... INFO @ Tue, 02 Aug 2022 15:17:37: start X-correlation... INFO @ Tue, 02 Aug 2022 15:17:37: end of X-cor INFO @ Tue, 02 Aug 2022 15:17:37: #2 finished! INFO @ Tue, 02 Aug 2022 15:17:37: #2 predicted fragment length is 140 bps INFO @ Tue, 02 Aug 2022 15:17:37: #2 alternative fragment length(s) may be 4,140 bps INFO @ Tue, 02 Aug 2022 15:17:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206491/SRX15206491.10_model.r WARNING @ Tue, 02 Aug 2022 15:17:37: #2 Since the d (140) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:17:37: #2 You may need to consider one of the other alternative d(s): 4,140 WARNING @ Tue, 02 Aug 2022 15:17:37: #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 15:17:37: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:17:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:17:46: 13000000 INFO @ Tue, 02 Aug 2022 15:17:56: 14000000 INFO @ Tue, 02 Aug 2022 15:18:02: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 15:18:02: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 15:18:02: #1 total tags in treatment: 14673768 INFO @ Tue, 02 Aug 2022 15:18:02: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:18:02: #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 15:18:03: #1 tags after filtering in treatment: 14673768 INFO @ Tue, 02 Aug 2022 15:18:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:18:03: #1 finished! INFO @ Tue, 02 Aug 2022 15:18:03: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:18:03: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 15:18:04: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:18:05: #2 number of paired peaks: 3858 INFO @ Tue, 02 Aug 2022 15:18:05: start model_add_line... INFO @ Tue, 02 Aug 2022 15:18:05: start X-correlation... INFO @ Tue, 02 Aug 2022 15:18:05: end of X-cor INFO @ Tue, 02 Aug 2022 15:18:05: #2 finished! INFO @ Tue, 02 Aug 2022 15:18:05: #2 predicted fragment length is 140 bps INFO @ Tue, 02 Aug 2022 15:18:05: #2 alternative fragment length(s) may be 4,140 bps INFO @ Tue, 02 Aug 2022 15:18:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206491/SRX15206491.20_model.r WARNING @ Tue, 02 Aug 2022 15:18:05: #2 Since the d (140) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:18:05: #2 You may need to consider one of the other alternative d(s): 4,140 WARNING @ Tue, 02 Aug 2022 15:18:05: #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 15:18:05: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:18:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:18:26: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:18:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206491/SRX15206491.05_peaks.xls INFO @ Tue, 02 Aug 2022 15:18:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206491/SRX15206491.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:18:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206491/SRX15206491.05_summits.bed INFO @ Tue, 02 Aug 2022 15:18:33: Done! pass1 - making usageList (14 chroms): 10 millis pass2 - checking and writing primary data (15457 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:18:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206491/SRX15206491.10_peaks.xls INFO @ Tue, 02 Aug 2022 15:18:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206491/SRX15206491.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:18:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206491/SRX15206491.10_summits.bed INFO @ Tue, 02 Aug 2022 15:18:51: Done! pass1 - making usageList (14 chroms): 8 millis pass2 - checking and writing primary data (8756 records, 4 fields): 44 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:18:54: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:19:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206491/SRX15206491.20_peaks.xls INFO @ Tue, 02 Aug 2022 15:19:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206491/SRX15206491.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:19:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206491/SRX15206491.20_summits.bed INFO @ Tue, 02 Aug 2022 15:19:19: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3559 records, 4 fields): 30 millis CompletedMACS2peakCalling