[2023-03-17 03:29:19,762] [INFO] DFAST_QC pipeline started.
[2023-03-17 03:29:19,762] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 03:29:19,762] [INFO] DQC Reference Directory: /var/lib/cwl/stg7c4ff7f6-c7dc-4b07-ad1a-02e2dd0c1ce0/dqc_reference
[2023-03-17 03:29:21,321] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 03:29:21,321] [INFO] Task started: Prodigal
[2023-03-17 03:29:21,322] [INFO] Running command: cat /var/lib/cwl/stgbe2ade07-b5f5-4c91-8d63-7c7748aed633/OceanDNA-b6718.fa | prodigal -d OceanDNA-b6718/cds.fna -a OceanDNA-b6718/protein.faa -g 11 -q > /dev/null
[2023-03-17 03:29:42,417] [INFO] Task succeeded: Prodigal
[2023-03-17 03:29:42,418] [INFO] Task started: HMMsearch
[2023-03-17 03:29:42,418] [INFO] Running command: hmmsearch --tblout OceanDNA-b6718/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7c4ff7f6-c7dc-4b07-ad1a-02e2dd0c1ce0/dqc_reference/reference_markers.hmm OceanDNA-b6718/protein.faa > /dev/null
[2023-03-17 03:29:42,634] [INFO] Task succeeded: HMMsearch
[2023-03-17 03:29:42,634] [INFO] Found 6/6 markers.
[2023-03-17 03:29:42,655] [INFO] Query marker FASTA was written to OceanDNA-b6718/markers.fasta
[2023-03-17 03:29:42,655] [INFO] Task started: Blastn
[2023-03-17 03:29:42,655] [INFO] Running command: blastn -query OceanDNA-b6718/markers.fasta -db /var/lib/cwl/stg7c4ff7f6-c7dc-4b07-ad1a-02e2dd0c1ce0/dqc_reference/reference_markers.fasta -out OceanDNA-b6718/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:29:43,213] [INFO] Task succeeded: Blastn
[2023-03-17 03:29:43,214] [INFO] Selected 29 target genomes.
[2023-03-17 03:29:43,214] [INFO] Target genome list was writen to OceanDNA-b6718/target_genomes.txt
[2023-03-17 03:29:43,225] [INFO] Task started: fastANI
[2023-03-17 03:29:43,225] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe2ade07-b5f5-4c91-8d63-7c7748aed633/OceanDNA-b6718.fa --refList OceanDNA-b6718/target_genomes.txt --output OceanDNA-b6718/fastani_result.tsv --threads 1
[2023-03-17 03:29:59,092] [INFO] Task succeeded: fastANI
[2023-03-17 03:29:59,092] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7c4ff7f6-c7dc-4b07-ad1a-02e2dd0c1ce0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 03:29:59,093] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7c4ff7f6-c7dc-4b07-ad1a-02e2dd0c1ce0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 03:29:59,102] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 03:29:59,102] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 03:29:59,102] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Muricauda parva	strain=DSM 25885	GCA_900215465.1	1247520	1247520	type	True	76.7535	123	1030	95	below_threshold
Croceivirga lutea	strain=CGMCC 1.15761	GCA_014643615.1	1775167	1775167	type	True	76.7272	162	1030	95	below_threshold
Croceivirga lutea	strain=CSW06	GCA_014235875.1	1775167	1775167	type	True	76.7265	161	1030	95	below_threshold
Croceivirga radicis	strain=HSG9	GCA_002072105.2	1929488	1929488	type	True	76.6545	151	1030	95	below_threshold
Muricauda zhangzhouensis	strain=DSM 25030	GCA_900106825.1	1073328	1073328	type	True	76.6176	118	1030	95	below_threshold
Muricauda zhangzhouensis	strain=CGMCC 1.11028	GCA_900102925.1	1073328	1073328	type	True	76.5821	120	1030	95	below_threshold
Muricauda amphidinii	strain=LMIT004	GCA_013090115.1	2735167	2735167	type	True	76.5209	125	1030	95	below_threshold
Muricauda aurantiaca	strain=HME9304	GCA_003269425.1	1383885	1383885	type	True	76.3314	110	1030	95	below_threshold
Croceitalea dokdonensis	strain=DOKDO 023	GCA_001306415.1	346188	346188	type	True	76.3219	93	1030	95	below_threshold
Maribacter dokdonensis	strain=DSW-8	GCA_001447995.1	320912	320912	type	True	76.2218	109	1030	95	below_threshold
Muricauda pacifica	strain=DSM 25027	GCA_003001695.1	1080225	1080225	type	True	76.2129	122	1030	95	below_threshold
Aurantibacter crassamenti	strain=HG732	GCA_016811105.1	1837375	1837375	type	True	75.919	88	1030	95	below_threshold
Saonia flava	strain=DSM 29762	GCA_011927795.1	523696	523696	type	True	75.8683	101	1030	95	below_threshold
Zobellia barbeyronii	strain=KMM 6746	GCA_018603515.1	2748009	2748009	type	True	75.8444	67	1030	95	below_threshold
Cellulophaga omnivescoria	strain=W5C	GCA_001999725.1	1888890	1888890	type	True	75.769	68	1030	95	below_threshold
Arenibacter latericius	strain=DSM 15913	GCA_000424985.1	86104	86104	type	True	75.7673	62	1030	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 03:29:59,102] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6718/tc_result.tsv
[2023-03-17 03:29:59,102] [INFO] ===== Taxonomy check completed =====
[2023-03-17 03:29:59,102] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 03:29:59,103] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7c4ff7f6-c7dc-4b07-ad1a-02e2dd0c1ce0/dqc_reference/checkm_data
[2023-03-17 03:29:59,103] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 03:29:59,108] [INFO] Task started: CheckM
[2023-03-17 03:29:59,108] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6718/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6718/checkm_input OceanDNA-b6718/checkm_result
[2023-03-17 03:30:52,699] [INFO] Task succeeded: CheckM
[2023-03-17 03:30:52,699] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 03:30:52,701] [INFO] ===== Completeness check finished =====
[2023-03-17 03:30:52,701] [INFO] ===== Start GTDB Search =====
[2023-03-17 03:30:52,701] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6718/markers.fasta)
[2023-03-17 03:30:52,702] [INFO] Task started: Blastn
[2023-03-17 03:30:52,702] [INFO] Running command: blastn -query OceanDNA-b6718/markers.fasta -db /var/lib/cwl/stg7c4ff7f6-c7dc-4b07-ad1a-02e2dd0c1ce0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6718/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:30:53,478] [INFO] Task succeeded: Blastn
[2023-03-17 03:30:53,479] [INFO] Selected 29 target genomes.
[2023-03-17 03:30:53,479] [INFO] Target genome list was writen to OceanDNA-b6718/target_genomes_gtdb.txt
[2023-03-17 03:30:53,589] [INFO] Task started: fastANI
[2023-03-17 03:30:53,590] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe2ade07-b5f5-4c91-8d63-7c7748aed633/OceanDNA-b6718.fa --refList OceanDNA-b6718/target_genomes_gtdb.txt --output OceanDNA-b6718/fastani_result_gtdb.tsv --threads 1
[2023-03-17 03:31:12,019] [INFO] Task succeeded: fastANI
[2023-03-17 03:31:12,031] [INFO] Found 23 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 03:31:12,031] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_009797885.1	s__Croceivirga sp009797885	77.2313	230	1030	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Croceivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012272815.1	s__Croceivirga sp012272815	76.9557	179	1030	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Croceivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900215465.1	s__Muricauda pacifica_A	76.7717	122	1030	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014235875.1	s__Croceivirga lutea	76.74	160	1030	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Croceivirga	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013090115.1	s__Muricauda amphidinii	76.5209	125	1030	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005144745.1	s__Croceivirga sp005144745	76.4654	145	1030	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Croceivirga	95.0	97.80	97.80	0.93	0.93	2	-
GCF_010993855.1	s__Muricauda sp010993855	76.4415	139	1030	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013001145.1	s__Croceitalea sp013001145	76.357	115	1030	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Croceitalea	95.0	99.20	99.17	0.87	0.85	5	-
GCF_018449435.1	s__Muricauda sp018449435	76.3518	115	1030	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003269425.1	s__Muricauda maritima	76.3314	110	1030	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017313225.1	s__Muricauda sp017313225	76.3243	108	1030	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001306415.1	s__Croceitalea dokdonensis	76.3219	93	1030	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Croceitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003149745.1	s__Muricauda koreensis	76.2567	141	1030	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003001695.1	s__Muricauda pacifica	76.227	121	1030	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001447995.1	s__Maribacter dokdonensis	76.2218	109	1030	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	97.64	97.51	0.89	0.86	13	-
GCF_008040165.1	s__Muricauda hymeniacidonis	76.1021	154	1030	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016811105.1	s__Aurantibacter_A crassamenti	75.919	88	1030	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aurantibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112245.1	s__Maribacter stanieri	75.8728	86	1030	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	98.09	98.09	0.92	0.92	2	-
GCF_011927795.1	s__Saonia flava	75.8683	101	1030	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Saonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018603515.1	s__Zobellia sp018603515	75.8444	67	1030	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019021925.1	s__Cellulophaga sp019021925	75.839	89	1030	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001999725.1	s__Cellulophaga omnivescoria	75.7564	67	1030	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Cellulophaga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009649685.1	s__Aurantibacter_A sp009649685	75.6873	93	1030	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aurantibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 03:31:12,032] [INFO] GTDB search result was written to OceanDNA-b6718/result_gtdb.tsv
[2023-03-17 03:31:12,032] [INFO] ===== GTDB Search completed =====
[2023-03-17 03:31:12,034] [INFO] DFAST_QC result json was written to OceanDNA-b6718/dqc_result.json
[2023-03-17 03:31:12,034] [INFO] DFAST_QC completed!
[2023-03-17 03:31:12,034] [INFO] Total running time: 0h1m52s