[2023-06-30 23:29:01,150] [INFO] DFAST_QC pipeline started.
[2023-06-30 23:29:01,153] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 23:29:01,153] [INFO] DQC Reference Directory: /var/lib/cwl/stgf529c1a2-6f1d-4365-b073-3a8f2b1bcd40/dqc_reference
[2023-06-30 23:29:04,038] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 23:29:04,039] [INFO] Task started: Prodigal
[2023-06-30 23:29:04,040] [INFO] Running command: gunzip -c /var/lib/cwl/stge5fbb83f-7c44-42f1-a316-30cedec1380b/GCA_024643855.1_ASM2464385v1_genomic.fna.gz | prodigal -d GCA_024643855.1_ASM2464385v1_genomic.fna/cds.fna -a GCA_024643855.1_ASM2464385v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 23:29:11,685] [INFO] Task succeeded: Prodigal
[2023-06-30 23:29:11,685] [INFO] Task started: HMMsearch
[2023-06-30 23:29:11,686] [INFO] Running command: hmmsearch --tblout GCA_024643855.1_ASM2464385v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf529c1a2-6f1d-4365-b073-3a8f2b1bcd40/dqc_reference/reference_markers.hmm GCA_024643855.1_ASM2464385v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 23:29:11,944] [INFO] Task succeeded: HMMsearch
[2023-06-30 23:29:11,946] [INFO] Found 6/6 markers.
[2023-06-30 23:29:11,980] [INFO] Query marker FASTA was written to GCA_024643855.1_ASM2464385v1_genomic.fna/markers.fasta
[2023-06-30 23:29:11,981] [INFO] Task started: Blastn
[2023-06-30 23:29:11,981] [INFO] Running command: blastn -query GCA_024643855.1_ASM2464385v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf529c1a2-6f1d-4365-b073-3a8f2b1bcd40/dqc_reference/reference_markers.fasta -out GCA_024643855.1_ASM2464385v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 23:29:12,596] [INFO] Task succeeded: Blastn
[2023-06-30 23:29:12,600] [INFO] Selected 34 target genomes.
[2023-06-30 23:29:12,601] [INFO] Target genome list was writen to GCA_024643855.1_ASM2464385v1_genomic.fna/target_genomes.txt
[2023-06-30 23:29:12,608] [INFO] Task started: fastANI
[2023-06-30 23:29:12,608] [INFO] Running command: fastANI --query /var/lib/cwl/stge5fbb83f-7c44-42f1-a316-30cedec1380b/GCA_024643855.1_ASM2464385v1_genomic.fna.gz --refList GCA_024643855.1_ASM2464385v1_genomic.fna/target_genomes.txt --output GCA_024643855.1_ASM2464385v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 23:29:32,553] [INFO] Task succeeded: fastANI
[2023-06-30 23:29:32,554] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf529c1a2-6f1d-4365-b073-3a8f2b1bcd40/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 23:29:32,555] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf529c1a2-6f1d-4365-b073-3a8f2b1bcd40/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 23:29:32,583] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2023-06-30 23:29:32,583] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-30 23:29:32,584] [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
Planktomarina temperata	strain=RCA23	GCA_000738435.1	1284658	1284658	type	True	98.9213	722	738	95	conclusive
Nereida ignava	strain=CECT 5292	GCA_001049735.1	282199	282199	type	True	76.3358	52	738	95	below_threshold
Nereida ignava	strain=DSM 16309	GCA_900114125.1	282199	282199	type	True	76.2897	50	738	95	below_threshold
Actibacterium atlanticum	strain=22II-S11-z10	GCA_000671395.1	1461693	1461693	type	True	76.1252	54	738	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	76.1201	80	738	95	below_threshold
Phaeobacter porticola	strain=P97	GCA_001888185.1	1844006	1844006	type	True	76.0842	70	738	95	below_threshold
Epibacterium ulvae	strain=U95	GCA_002796795.1	1156985	1156985	type	True	75.9771	60	738	95	below_threshold
Epibacterium ulvae	strain=U95	GCA_900102795.1	1156985	1156985	type	True	75.9606	61	738	95	below_threshold
Pelagicola litoralis	strain=CL-ES2	GCA_005518135.1	420403	420403	type	True	75.9556	58	738	95	below_threshold
Puniceibacterium antarcticum	strain=SM1211	GCA_002760615.1	1206336	1206336	type	True	75.9091	54	738	95	below_threshold
Roseovarius marisflavi	strain=DSM 29327	GCA_900142625.1	1054996	1054996	type	True	75.8515	73	738	95	below_threshold
Sulfitobacter brevis	strain=DSM 11443	GCA_900112755.1	74348	74348	type	True	75.8495	58	738	95	below_threshold
Tritonibacter multivorans	strain=CECT 7557	GCA_001458415.1	928856	928856	type	True	75.8308	82	738	95	below_threshold
Leisingera methylohalidivorans	strain=DSM 14336; MB2	GCA_000511355.1	133924	133924	type	True	75.8279	59	738	95	below_threshold
Pelagivirga sediminicola	strain=BH-SD19	GCA_003072125.1	2170575	2170575	type	True	75.8172	55	738	95	below_threshold
Tritonibacter litoralis	strain=SM1979	GCA_009496005.1	2662264	2662264	type	True	75.8008	69	738	95	below_threshold
Aestuariivita boseongensis	strain=BS-B2	GCA_001262635.1	1470562	1470562	type	True	75.6601	76	738	95	below_threshold
Pseudoprimorskyibacter insulae	strain=CECT 8871	GCA_900302505.1	1695997	1695997	type	True	75.6265	59	738	95	below_threshold
Rhabdonatronobacter sediminivivens	strain=IM2376	GCA_013415485.1	2743469	2743469	type	True	75.5816	51	738	95	below_threshold
Roseovarius gaetbuli	strain=CECT 8370	GCA_900172365.1	1356575	1356575	type	True	75.5479	83	738	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	75.5039	61	738	95	below_threshold
Pseudorhodobacter turbinis	strain=S12M18	GCA_005234135.1	2500533	2500533	type	True	75.4789	55	738	95	below_threshold
Roseovarius gahaiensis	strain=GH877	GCA_011601345.1	2716691	2716691	type	True	75.4756	63	738	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 23:29:32,587] [INFO] DFAST Taxonomy check result was written to GCA_024643855.1_ASM2464385v1_genomic.fna/tc_result.tsv
[2023-06-30 23:29:32,588] [INFO] ===== Taxonomy check completed =====
[2023-06-30 23:29:32,588] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 23:29:32,588] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf529c1a2-6f1d-4365-b073-3a8f2b1bcd40/dqc_reference/checkm_data
[2023-06-30 23:29:32,590] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 23:29:32,619] [INFO] Task started: CheckM
[2023-06-30 23:29:32,619] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024643855.1_ASM2464385v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024643855.1_ASM2464385v1_genomic.fna/checkm_input GCA_024643855.1_ASM2464385v1_genomic.fna/checkm_result
[2023-06-30 23:30:00,883] [INFO] Task succeeded: CheckM
[2023-06-30 23:30:00,884] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 23:30:00,907] [INFO] ===== Completeness check finished =====
[2023-06-30 23:30:00,908] [INFO] ===== Start GTDB Search =====
[2023-06-30 23:30:00,908] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024643855.1_ASM2464385v1_genomic.fna/markers.fasta)
[2023-06-30 23:30:00,909] [INFO] Task started: Blastn
[2023-06-30 23:30:00,909] [INFO] Running command: blastn -query GCA_024643855.1_ASM2464385v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf529c1a2-6f1d-4365-b073-3a8f2b1bcd40/dqc_reference/reference_markers_gtdb.fasta -out GCA_024643855.1_ASM2464385v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 23:30:01,779] [INFO] Task succeeded: Blastn
[2023-06-30 23:30:01,783] [INFO] Selected 9 target genomes.
[2023-06-30 23:30:01,784] [INFO] Target genome list was writen to GCA_024643855.1_ASM2464385v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 23:30:01,791] [INFO] Task started: fastANI
[2023-06-30 23:30:01,791] [INFO] Running command: fastANI --query /var/lib/cwl/stge5fbb83f-7c44-42f1-a316-30cedec1380b/GCA_024643855.1_ASM2464385v1_genomic.fna.gz --refList GCA_024643855.1_ASM2464385v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024643855.1_ASM2464385v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 23:30:06,922] [INFO] Task succeeded: fastANI
[2023-06-30 23:30:06,933] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 23:30:06,933] [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
GCF_000738435.1	s__Planktomarina temperata	98.9213	722	738	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktomarina	95.0	98.99	97.76	0.97	0.80	20	conclusive
GCA_016780825.1	s__Planktomarina sp016780825	90.5147	634	738	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905181815.1	s__Planktomarina sp905181815	89.9886	647	738	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002683685.1	s__Planktomarina sp002683685	87.1291	497	738	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktomarina	95.0	95.59	95.45	0.70	0.67	6	-
GCA_905182455.1	s__Planktomarina sp905182455	78.006	301	738	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktomarina	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000981705.1	s__Planktomarina sp000981705	77.5716	173	738	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktomarina	95.0	98.80	98.80	0.86	0.86	2	-
GCF_001458175.1	s__Shimia marina	75.8677	68	738	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Shimia	95.0	98.13	96.28	0.94	0.89	3	-
GCF_011601345.1	s__Roseovarius gahaiensis	75.4421	65	738	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 23:30:06,935] [INFO] GTDB search result was written to GCA_024643855.1_ASM2464385v1_genomic.fna/result_gtdb.tsv
[2023-06-30 23:30:06,936] [INFO] ===== GTDB Search completed =====
[2023-06-30 23:30:06,940] [INFO] DFAST_QC result json was written to GCA_024643855.1_ASM2464385v1_genomic.fna/dqc_result.json
[2023-06-30 23:30:06,940] [INFO] DFAST_QC completed!
[2023-06-30 23:30:06,940] [INFO] Total running time: 0h1m6s