Job ID = 16438940 SRX = ERX9184108 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T05:12:24 prefetch.2.10.7: 1) Downloading 'ERR9630955'... 2022-08-02T05:12:24 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T05:14:27 prefetch.2.10.7: HTTPS download succeed 2022-08-02T05:14:27 prefetch.2.10.7: 1) 'ERR9630955' was downloaded successfully 2022-08-02T05:14:27 prefetch.2.10.7: 'ERR9630955' has 0 unresolved dependencies Read 53977751 spots for ERR9630955/ERR9630955.sra Written 53977751 spots for ERR9630955/ERR9630955.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439164 ("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: 00:19:27 53977751 reads; of these: 53977751 (100.00%) were unpaired; of these: 3135955 (5.81%) aligned 0 times 44115453 (81.73%) aligned exactly 1 time 6726343 (12.46%) aligned >1 times 94.19% overall alignment rate Time searching: 00:19:28 Overall time: 00:19:28 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 24 files... [bam_rmdupse_core] 26872037 / 50841796 = 0.5285 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 14:50:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX9184108/ERX9184108.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX9184108/ERX9184108.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX9184108/ERX9184108.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX9184108/ERX9184108.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 14:50:19: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:50:19: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:50:26: 1000000 INFO @ Tue, 02 Aug 2022 14:50:32: 2000000 INFO @ Tue, 02 Aug 2022 14:50:39: 3000000 INFO @ Tue, 02 Aug 2022 14:50:45: 4000000 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 14:50:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX9184108/ERX9184108.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX9184108/ERX9184108.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX9184108/ERX9184108.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX9184108/ERX9184108.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 14:50:48: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:50:48: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:50:52: 5000000 INFO @ Tue, 02 Aug 2022 14:50:56: 1000000 INFO @ Tue, 02 Aug 2022 14:50:59: 6000000 INFO @ Tue, 02 Aug 2022 14:51:04: 2000000 INFO @ Tue, 02 Aug 2022 14:51:06: 7000000 INFO @ Tue, 02 Aug 2022 14:51:12: 3000000 INFO @ Tue, 02 Aug 2022 14:51:13: 8000000 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 14:51:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX9184108/ERX9184108.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX9184108/ERX9184108.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX9184108/ERX9184108.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX9184108/ERX9184108.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 14:51:18: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:51:18: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:51:20: 4000000 INFO @ Tue, 02 Aug 2022 14:51:20: 9000000 INFO @ Tue, 02 Aug 2022 14:51:25: 1000000 INFO @ Tue, 02 Aug 2022 14:51:28: 5000000 INFO @ Tue, 02 Aug 2022 14:51:28: 10000000 INFO @ Tue, 02 Aug 2022 14:51:33: 2000000 INFO @ Tue, 02 Aug 2022 14:51:35: 6000000 INFO @ Tue, 02 Aug 2022 14:51:35: 11000000 INFO @ Tue, 02 Aug 2022 14:51:40: 3000000 INFO @ Tue, 02 Aug 2022 14:51:42: 7000000 INFO @ Tue, 02 Aug 2022 14:51:42: 12000000 INFO @ Tue, 02 Aug 2022 14:51:47: 4000000 INFO @ Tue, 02 Aug 2022 14:51:49: 13000000 INFO @ Tue, 02 Aug 2022 14:51:49: 8000000 INFO @ Tue, 02 Aug 2022 14:51:54: 5000000 INFO @ Tue, 02 Aug 2022 14:51:56: 14000000 INFO @ Tue, 02 Aug 2022 14:51:56: 9000000 INFO @ Tue, 02 Aug 2022 14:52:01: 6000000 INFO @ Tue, 02 Aug 2022 14:52:03: 15000000 INFO @ Tue, 02 Aug 2022 14:52:03: 10000000 INFO @ Tue, 02 Aug 2022 14:52:08: 7000000 INFO @ Tue, 02 Aug 2022 14:52:10: 16000000 INFO @ Tue, 02 Aug 2022 14:52:10: 11000000 INFO @ Tue, 02 Aug 2022 14:52:15: 8000000 INFO @ Tue, 02 Aug 2022 14:52:17: 17000000 INFO @ Tue, 02 Aug 2022 14:52:17: 12000000 INFO @ Tue, 02 Aug 2022 14:52:23: 9000000 INFO @ Tue, 02 Aug 2022 14:52:24: 18000000 INFO @ Tue, 02 Aug 2022 14:52:25: 13000000 INFO @ Tue, 02 Aug 2022 14:52:30: 10000000 INFO @ Tue, 02 Aug 2022 14:52:31: 19000000 INFO @ Tue, 02 Aug 2022 14:52:32: 14000000 INFO @ Tue, 02 Aug 2022 14:52:37: 11000000 INFO @ Tue, 02 Aug 2022 14:52:38: 20000000 INFO @ Tue, 02 Aug 2022 14:52:39: 15000000 INFO @ Tue, 02 Aug 2022 14:52:44: 12000000 INFO @ Tue, 02 Aug 2022 14:52:45: 21000000 INFO @ Tue, 02 Aug 2022 14:52:46: 16000000 INFO @ Tue, 02 Aug 2022 14:52:51: 13000000 INFO @ Tue, 02 Aug 2022 14:52:52: 22000000 INFO @ Tue, 02 Aug 2022 14:52:52: 17000000 INFO @ Tue, 02 Aug 2022 14:52:57: 14000000 INFO @ Tue, 02 Aug 2022 14:52:59: 23000000 INFO @ Tue, 02 Aug 2022 14:53:00: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:53:05: 15000000 INFO @ Tue, 02 Aug 2022 14:53:06: #1 tag size is determined as 81 bps INFO @ Tue, 02 Aug 2022 14:53:06: #1 tag size = 81 INFO @ Tue, 02 Aug 2022 14:53:06: #1 total tags in treatment: 23969759 INFO @ Tue, 02 Aug 2022 14:53:06: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:53:06: #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 14:53:07: #1 tags after filtering in treatment: 23969759 INFO @ Tue, 02 Aug 2022 14:53:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:53:07: #1 finished! INFO @ Tue, 02 Aug 2022 14:53:07: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:53:07: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:53:07: 19000000 INFO @ Tue, 02 Aug 2022 14:53:09: #2 number of paired peaks: 10947 INFO @ Tue, 02 Aug 2022 14:53:09: start model_add_line... INFO @ Tue, 02 Aug 2022 14:53:09: start X-correlation... INFO @ Tue, 02 Aug 2022 14:53:10: end of X-cor INFO @ Tue, 02 Aug 2022 14:53:10: #2 finished! INFO @ Tue, 02 Aug 2022 14:53:10: #2 predicted fragment length is 95 bps INFO @ Tue, 02 Aug 2022 14:53:10: #2 alternative fragment length(s) may be 95 bps INFO @ Tue, 02 Aug 2022 14:53:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX9184108/ERX9184108.05_model.r WARNING @ Tue, 02 Aug 2022 14:53:10: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:53:10: #2 You may need to consider one of the other alternative d(s): 95 WARNING @ Tue, 02 Aug 2022 14:53:10: #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 14:53:10: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:53:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:53:11: 16000000 INFO @ Tue, 02 Aug 2022 14:53:14: 20000000 INFO @ Tue, 02 Aug 2022 14:53:18: 17000000 INFO @ Tue, 02 Aug 2022 14:53:21: 21000000 INFO @ Tue, 02 Aug 2022 14:53:25: 18000000 INFO @ Tue, 02 Aug 2022 14:53:28: 22000000 INFO @ Tue, 02 Aug 2022 14:53:32: 19000000 INFO @ Tue, 02 Aug 2022 14:53:35: 23000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:53:39: 20000000 INFO @ Tue, 02 Aug 2022 14:53:41: #1 tag size is determined as 81 bps INFO @ Tue, 02 Aug 2022 14:53:41: #1 tag size = 81 INFO @ Tue, 02 Aug 2022 14:53:41: #1 total tags in treatment: 23969759 INFO @ Tue, 02 Aug 2022 14:53:41: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:53:41: #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 14:53:42: #1 tags after filtering in treatment: 23969759 INFO @ Tue, 02 Aug 2022 14:53:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:53:42: #1 finished! INFO @ Tue, 02 Aug 2022 14:53:42: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:53:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:53:44: #2 number of paired peaks: 10947 INFO @ Tue, 02 Aug 2022 14:53:44: start model_add_line... INFO @ Tue, 02 Aug 2022 14:53:45: start X-correlation... INFO @ Tue, 02 Aug 2022 14:53:45: end of X-cor INFO @ Tue, 02 Aug 2022 14:53:45: #2 finished! INFO @ Tue, 02 Aug 2022 14:53:45: #2 predicted fragment length is 95 bps INFO @ Tue, 02 Aug 2022 14:53:45: #2 alternative fragment length(s) may be 95 bps INFO @ Tue, 02 Aug 2022 14:53:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX9184108/ERX9184108.10_model.r WARNING @ Tue, 02 Aug 2022 14:53:45: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:53:45: #2 You may need to consider one of the other alternative d(s): 95 WARNING @ Tue, 02 Aug 2022 14:53:45: #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 14:53:45: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:53:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:53:46: 21000000 INFO @ Tue, 02 Aug 2022 14:53:52: 22000000 INFO @ Tue, 02 Aug 2022 14:53:57: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:53:59: 23000000 INFO @ Tue, 02 Aug 2022 14:54:05: #1 tag size is determined as 81 bps INFO @ Tue, 02 Aug 2022 14:54:05: #1 tag size = 81 INFO @ Tue, 02 Aug 2022 14:54:05: #1 total tags in treatment: 23969759 INFO @ Tue, 02 Aug 2022 14:54:05: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:54:05: #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 14:54:05: #1 tags after filtering in treatment: 23969759 INFO @ Tue, 02 Aug 2022 14:54:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:54:05: #1 finished! INFO @ Tue, 02 Aug 2022 14:54:05: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:54:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:54:08: #2 number of paired peaks: 10947 INFO @ Tue, 02 Aug 2022 14:54:08: start model_add_line... INFO @ Tue, 02 Aug 2022 14:54:08: start X-correlation... INFO @ Tue, 02 Aug 2022 14:54:08: end of X-cor INFO @ Tue, 02 Aug 2022 14:54:08: #2 finished! INFO @ Tue, 02 Aug 2022 14:54:08: #2 predicted fragment length is 95 bps INFO @ Tue, 02 Aug 2022 14:54:08: #2 alternative fragment length(s) may be 95 bps INFO @ Tue, 02 Aug 2022 14:54:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX9184108/ERX9184108.20_model.r WARNING @ Tue, 02 Aug 2022 14:54:08: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:54:08: #2 You may need to consider one of the other alternative d(s): 95 WARNING @ Tue, 02 Aug 2022 14:54:08: #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 14:54:08: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:54:08: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:54:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX9184108/ERX9184108.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:54:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX9184108/ERX9184108.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:54:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX9184108/ERX9184108.05_summits.bed INFO @ Tue, 02 Aug 2022 14:54:20: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (12014 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:54:33: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:54:54: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:54:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX9184108/ERX9184108.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:54:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX9184108/ERX9184108.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:54:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX9184108/ERX9184108.10_summits.bed INFO @ Tue, 02 Aug 2022 14:54:55: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (10215 records, 4 fields): 30 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:55:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX9184108/ERX9184108.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:55:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX9184108/ERX9184108.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:55:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX9184108/ERX9184108.20_summits.bed INFO @ Tue, 02 Aug 2022 14:55:16: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (7943 records, 4 fields): 26 millis CompletedMACS2peakCalling