Job ID = 16439273 SRX = SRX15206478 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T05:48:17 prefetch.2.10.7: 1) Downloading 'SRR19139326'... 2022-08-02T05:48:17 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T05:48:54 prefetch.2.10.7: HTTPS download succeed 2022-08-02T05:48:54 prefetch.2.10.7: 1) 'SRR19139326' was downloaded successfully 2022-08-02T05:48:54 prefetch.2.10.7: 'SRR19139326' has 0 unresolved dependencies Read 9842119 spots for SRR19139326/SRR19139326.sra Written 9842119 spots for SRR19139326/SRR19139326.sra 2022-08-02T05:49:34 prefetch.2.10.7: 1) Downloading 'SRR19139327'... 2022-08-02T05:49:34 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T05:50:19 prefetch.2.10.7: HTTPS download succeed 2022-08-02T05:50:20 prefetch.2.10.7: 'SRR19139327' is valid 2022-08-02T05:50:20 prefetch.2.10.7: 1) 'SRR19139327' was downloaded successfully 2022-08-02T05:50:20 prefetch.2.10.7: 'SRR19139327' has 0 unresolved dependencies Read 9842119 spots for SRR19139327/SRR19139327.sra Written 9842119 spots for SRR19139327/SRR19139327.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439434 ("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: 00:15:50 19684238 reads; of these: 19684238 (100.00%) were unpaired; of these: 1257058 (6.39%) aligned 0 times 10486182 (53.27%) aligned exactly 1 time 7940998 (40.34%) aligned >1 times 93.61% overall alignment rate Time searching: 00:15:50 Overall time: 00:15:50 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 16 files... [bam_rmdupse_core] 10328448 / 18427180 = 0.5605 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 15:13:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206478/SRX15206478.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206478/SRX15206478.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206478/SRX15206478.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206478/SRX15206478.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 15:13:57: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:13:57: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:14:07: 1000000 INFO @ Tue, 02 Aug 2022 15:14:18: 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 15:14:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206478/SRX15206478.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206478/SRX15206478.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206478/SRX15206478.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206478/SRX15206478.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 15:14:26: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:14:26: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:14:28: 3000000 INFO @ Tue, 02 Aug 2022 15:14:37: 1000000 INFO @ Tue, 02 Aug 2022 15:14:39: 4000000 INFO @ Tue, 02 Aug 2022 15:14:47: 2000000 INFO @ Tue, 02 Aug 2022 15:14:50: 5000000 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 15:14:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206478/SRX15206478.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206478/SRX15206478.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206478/SRX15206478.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206478/SRX15206478.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 15:14:56: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:14:56: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:14:57: 3000000 INFO @ Tue, 02 Aug 2022 15:15:02: 6000000 INFO @ Tue, 02 Aug 2022 15:15:07: 1000000 INFO @ Tue, 02 Aug 2022 15:15:08: 4000000 INFO @ Tue, 02 Aug 2022 15:15:13: 7000000 INFO @ Tue, 02 Aug 2022 15:15:18: 2000000 INFO @ Tue, 02 Aug 2022 15:15:18: 5000000 INFO @ Tue, 02 Aug 2022 15:15:24: 8000000 INFO @ Tue, 02 Aug 2022 15:15:25: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 15:15:25: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 15:15:25: #1 total tags in treatment: 8098732 INFO @ Tue, 02 Aug 2022 15:15:25: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:15:25: #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 15:15:25: #1 tags after filtering in treatment: 8098732 INFO @ Tue, 02 Aug 2022 15:15:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:15:25: #1 finished! INFO @ Tue, 02 Aug 2022 15:15:25: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:15:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:15:26: #2 number of paired peaks: 6311 INFO @ Tue, 02 Aug 2022 15:15:26: start model_add_line... INFO @ Tue, 02 Aug 2022 15:15:26: start X-correlation... INFO @ Tue, 02 Aug 2022 15:15:26: end of X-cor INFO @ Tue, 02 Aug 2022 15:15:26: #2 finished! INFO @ Tue, 02 Aug 2022 15:15:26: #2 predicted fragment length is 218 bps INFO @ Tue, 02 Aug 2022 15:15:26: #2 alternative fragment length(s) may be 218 bps INFO @ Tue, 02 Aug 2022 15:15:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206478/SRX15206478.05_model.r WARNING @ Tue, 02 Aug 2022 15:15:26: #2 Since the d (218) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:15:26: #2 You may need to consider one of the other alternative d(s): 218 WARNING @ Tue, 02 Aug 2022 15:15:26: #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 15:15:26: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:15:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:15:28: 3000000 INFO @ Tue, 02 Aug 2022 15:15:29: 6000000 INFO @ Tue, 02 Aug 2022 15:15:38: 4000000 INFO @ Tue, 02 Aug 2022 15:15:39: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 15:15:48: 5000000 INFO @ Tue, 02 Aug 2022 15:15:49: 8000000 INFO @ Tue, 02 Aug 2022 15:15:50: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 15:15:50: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 15:15:50: #1 total tags in treatment: 8098732 INFO @ Tue, 02 Aug 2022 15:15:50: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:15:50: #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 15:15:50: #1 tags after filtering in treatment: 8098732 INFO @ Tue, 02 Aug 2022 15:15:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:15:50: #1 finished! INFO @ Tue, 02 Aug 2022 15:15:50: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:15:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:15:51: #2 number of paired peaks: 6311 INFO @ Tue, 02 Aug 2022 15:15:51: start model_add_line... INFO @ Tue, 02 Aug 2022 15:15:51: start X-correlation... INFO @ Tue, 02 Aug 2022 15:15:51: end of X-cor INFO @ Tue, 02 Aug 2022 15:15:51: #2 finished! INFO @ Tue, 02 Aug 2022 15:15:51: #2 predicted fragment length is 218 bps INFO @ Tue, 02 Aug 2022 15:15:51: #2 alternative fragment length(s) may be 218 bps INFO @ Tue, 02 Aug 2022 15:15:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206478/SRX15206478.10_model.r WARNING @ Tue, 02 Aug 2022 15:15:51: #2 Since the d (218) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:15:51: #2 You may need to consider one of the other alternative d(s): 218 WARNING @ Tue, 02 Aug 2022 15:15:51: #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 15:15:51: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:15:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:15:52: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 15:15:57: 6000000 INFO @ Tue, 02 Aug 2022 15:16:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206478/SRX15206478.05_peaks.xls INFO @ Tue, 02 Aug 2022 15:16:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206478/SRX15206478.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:16:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206478/SRX15206478.05_summits.bed INFO @ Tue, 02 Aug 2022 15:16:02: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (9477 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:16:06: 7000000 INFO @ Tue, 02 Aug 2022 15:16:15: 8000000 INFO @ Tue, 02 Aug 2022 15:16:16: #1 tag size is determined as 150 bps INFO @ Tue, 02 Aug 2022 15:16:16: #1 tag size = 150 INFO @ Tue, 02 Aug 2022 15:16:16: #1 total tags in treatment: 8098732 INFO @ Tue, 02 Aug 2022 15:16:16: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:16:16: #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 15:16:16: #1 tags after filtering in treatment: 8098732 INFO @ Tue, 02 Aug 2022 15:16:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:16:16: #1 finished! INFO @ Tue, 02 Aug 2022 15:16:16: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:16:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:16:17: #2 number of paired peaks: 6311 INFO @ Tue, 02 Aug 2022 15:16:17: start model_add_line... INFO @ Tue, 02 Aug 2022 15:16:17: start X-correlation... INFO @ Tue, 02 Aug 2022 15:16:17: end of X-cor INFO @ Tue, 02 Aug 2022 15:16:17: #2 finished! INFO @ Tue, 02 Aug 2022 15:16:17: #2 predicted fragment length is 218 bps INFO @ Tue, 02 Aug 2022 15:16:17: #2 alternative fragment length(s) may be 218 bps INFO @ Tue, 02 Aug 2022 15:16:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206478/SRX15206478.20_model.r WARNING @ Tue, 02 Aug 2022 15:16:18: #2 Since the d (218) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:16:18: #2 You may need to consider one of the other alternative d(s): 218 WARNING @ Tue, 02 Aug 2022 15:16:18: #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 15:16:18: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:16:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:16:18: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:16:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206478/SRX15206478.10_peaks.xls INFO @ Tue, 02 Aug 2022 15:16:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206478/SRX15206478.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:16:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206478/SRX15206478.10_summits.bed INFO @ Tue, 02 Aug 2022 15:16:29: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6893 records, 4 fields): 46 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:16:43: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:16:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206478/SRX15206478.20_peaks.xls INFO @ Tue, 02 Aug 2022 15:16:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206478/SRX15206478.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:16:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206478/SRX15206478.20_summits.bed INFO @ Tue, 02 Aug 2022 15:16:52: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4259 records, 4 fields): 6 millis CompletedMACS2peakCalling