Job ID = 16439317 SRX = SRX15206495 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T05:53:01 prefetch.2.10.7: 1) Downloading 'SRR19139299'... 2022-08-02T05:53:02 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T05:53:15 prefetch.2.10.7: HTTPS download succeed 2022-08-02T05:53:16 prefetch.2.10.7: 'SRR19139299' is valid 2022-08-02T05:53:16 prefetch.2.10.7: 1) 'SRR19139299' was downloaded successfully 2022-08-02T05:53:16 prefetch.2.10.7: 'SRR19139299' has 0 unresolved dependencies Read 7110873 spots for SRR19139299/SRR19139299.sra Written 7110873 spots for SRR19139299/SRR19139299.sra 2022-08-02T05:53:46 prefetch.2.10.7: 1) Downloading 'SRR19139300'... 2022-08-02T05:53:46 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T05:53:59 prefetch.2.10.7: HTTPS download succeed 2022-08-02T05:54:00 prefetch.2.10.7: 'SRR19139300' is valid 2022-08-02T05:54:00 prefetch.2.10.7: 1) 'SRR19139300' was downloaded successfully 2022-08-02T05:54:00 prefetch.2.10.7: 'SRR19139300' has 0 unresolved dependencies Read 7110873 spots for SRR19139300/SRR19139300.sra Written 7110873 spots for SRR19139300/SRR19139300.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439398 ("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: 00:06:46 14221746 reads; of these: 14221746 (100.00%) were unpaired; of these: 1036777 (7.29%) aligned 0 times 7777815 (54.69%) aligned exactly 1 time 5407154 (38.02%) aligned >1 times 92.71% overall alignment rate Time searching: 00:06:46 Overall time: 00:06:46 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] 3085765 / 13184969 = 0.2340 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 15:05:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206495/SRX15206495.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206495/SRX15206495.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206495/SRX15206495.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206495/SRX15206495.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 15:05:55: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:05:55: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:06:02: 1000000 INFO @ Tue, 02 Aug 2022 15:06:09: 2000000 INFO @ Tue, 02 Aug 2022 15:06:16: 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 15:06:22: 4000000 INFO @ Tue, 02 Aug 2022 15:06:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206495/SRX15206495.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206495/SRX15206495.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206495/SRX15206495.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206495/SRX15206495.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 15:06:24: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:06:24: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:06:30: 5000000 INFO @ Tue, 02 Aug 2022 15:06:30: 1000000 INFO @ Tue, 02 Aug 2022 15:06:36: 2000000 INFO @ Tue, 02 Aug 2022 15:06:37: 6000000 INFO @ Tue, 02 Aug 2022 15:06:42: 3000000 INFO @ Tue, 02 Aug 2022 15:06:44: 7000000 INFO @ Tue, 02 Aug 2022 15:06:48: 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 15:06:52: 8000000 INFO @ Tue, 02 Aug 2022 15:06:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206495/SRX15206495.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206495/SRX15206495.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206495/SRX15206495.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206495/SRX15206495.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 15:06:54: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:06:54: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:06:54: 5000000 INFO @ Tue, 02 Aug 2022 15:07:00: 9000000 INFO @ Tue, 02 Aug 2022 15:07:01: 6000000 INFO @ Tue, 02 Aug 2022 15:07:01: 1000000 INFO @ Tue, 02 Aug 2022 15:07:07: 10000000 INFO @ Tue, 02 Aug 2022 15:07:07: 7000000 INFO @ Tue, 02 Aug 2022 15:07:08: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 15:07:08: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 15:07:08: #1 total tags in treatment: 10099204 INFO @ Tue, 02 Aug 2022 15:07:08: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:07:08: #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 15:07:08: #1 tags after filtering in treatment: 10099204 INFO @ Tue, 02 Aug 2022 15:07:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:07:08: #1 finished! INFO @ Tue, 02 Aug 2022 15:07:08: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:07:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:07:08: 2000000 INFO @ Tue, 02 Aug 2022 15:07:09: #2 number of paired peaks: 1517 INFO @ Tue, 02 Aug 2022 15:07:09: start model_add_line... INFO @ Tue, 02 Aug 2022 15:07:09: start X-correlation... INFO @ Tue, 02 Aug 2022 15:07:09: end of X-cor INFO @ Tue, 02 Aug 2022 15:07:09: #2 finished! INFO @ Tue, 02 Aug 2022 15:07:09: #2 predicted fragment length is 146 bps INFO @ Tue, 02 Aug 2022 15:07:09: #2 alternative fragment length(s) may be 146 bps INFO @ Tue, 02 Aug 2022 15:07:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206495/SRX15206495.05_model.r WARNING @ Tue, 02 Aug 2022 15:07:09: #2 Since the d (146) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:07:09: #2 You may need to consider one of the other alternative d(s): 146 WARNING @ Tue, 02 Aug 2022 15:07:09: #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 15:07:09: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:07:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:07:15: 8000000 INFO @ Tue, 02 Aug 2022 15:07:15: 3000000 INFO @ Tue, 02 Aug 2022 15:07:22: 9000000 INFO @ Tue, 02 Aug 2022 15:07:23: 4000000 INFO @ Tue, 02 Aug 2022 15:07:29: 10000000 INFO @ Tue, 02 Aug 2022 15:07:29: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 15:07:29: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 15:07:29: #1 total tags in treatment: 10099204 INFO @ Tue, 02 Aug 2022 15:07:29: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:07:29: #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 15:07:30: #1 tags after filtering in treatment: 10099204 INFO @ Tue, 02 Aug 2022 15:07:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:07:30: #1 finished! INFO @ Tue, 02 Aug 2022 15:07:30: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:07:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:07:30: 5000000 INFO @ Tue, 02 Aug 2022 15:07:30: #2 number of paired peaks: 1517 INFO @ Tue, 02 Aug 2022 15:07:30: start model_add_line... INFO @ Tue, 02 Aug 2022 15:07:30: start X-correlation... INFO @ Tue, 02 Aug 2022 15:07:30: end of X-cor INFO @ Tue, 02 Aug 2022 15:07:30: #2 finished! INFO @ Tue, 02 Aug 2022 15:07:30: #2 predicted fragment length is 146 bps INFO @ Tue, 02 Aug 2022 15:07:30: #2 alternative fragment length(s) may be 146 bps INFO @ Tue, 02 Aug 2022 15:07:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206495/SRX15206495.10_model.r WARNING @ Tue, 02 Aug 2022 15:07:30: #2 Since the d (146) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:07:30: #2 You may need to consider one of the other alternative d(s): 146 WARNING @ Tue, 02 Aug 2022 15:07:30: #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 15:07:30: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:07:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:07:32: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:07:37: 6000000 INFO @ Tue, 02 Aug 2022 15:07:43: 7000000 INFO @ Tue, 02 Aug 2022 15:07:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206495/SRX15206495.05_peaks.xls INFO @ Tue, 02 Aug 2022 15:07:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206495/SRX15206495.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:07:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206495/SRX15206495.05_summits.bed INFO @ Tue, 02 Aug 2022 15:07:44: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5618 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:07:50: 8000000 INFO @ Tue, 02 Aug 2022 15:07:52: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:07:57: 9000000 INFO @ Tue, 02 Aug 2022 15:08:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206495/SRX15206495.10_peaks.xls INFO @ Tue, 02 Aug 2022 15:08:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206495/SRX15206495.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:08:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206495/SRX15206495.10_summits.bed INFO @ Tue, 02 Aug 2022 15:08:03: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2257 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:08:04: 10000000 INFO @ Tue, 02 Aug 2022 15:08:05: #1 tag size is determined as 75 bps INFO @ Tue, 02 Aug 2022 15:08:05: #1 tag size = 75 INFO @ Tue, 02 Aug 2022 15:08:05: #1 total tags in treatment: 10099204 INFO @ Tue, 02 Aug 2022 15:08:05: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:08:05: #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 15:08:05: #1 tags after filtering in treatment: 10099204 INFO @ Tue, 02 Aug 2022 15:08:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:08:05: #1 finished! INFO @ Tue, 02 Aug 2022 15:08:05: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:08:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:08:06: #2 number of paired peaks: 1517 INFO @ Tue, 02 Aug 2022 15:08:06: start model_add_line... INFO @ Tue, 02 Aug 2022 15:08:06: start X-correlation... INFO @ Tue, 02 Aug 2022 15:08:06: end of X-cor INFO @ Tue, 02 Aug 2022 15:08:06: #2 finished! INFO @ Tue, 02 Aug 2022 15:08:06: #2 predicted fragment length is 146 bps INFO @ Tue, 02 Aug 2022 15:08:06: #2 alternative fragment length(s) may be 146 bps INFO @ Tue, 02 Aug 2022 15:08:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206495/SRX15206495.20_model.r WARNING @ Tue, 02 Aug 2022 15:08:06: #2 Since the d (146) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:08:06: #2 You may need to consider one of the other alternative d(s): 146 WARNING @ Tue, 02 Aug 2022 15:08:06: #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 15:08:06: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:08:06: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 15:08:28: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:08:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206495/SRX15206495.20_peaks.xls INFO @ Tue, 02 Aug 2022 15:08:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206495/SRX15206495.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:08:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206495/SRX15206495.20_summits.bed INFO @ Tue, 02 Aug 2022 15:08:39: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (867 records, 4 fields): 15 millis CompletedMACS2peakCalling BigWig に変換しました。