[2024-01-24 12:23:03,951] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:23:03,953] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:23:03,953] [INFO] DQC Reference Directory: /var/lib/cwl/stgc7bfee3a-3304-4d71-8489-ffb5754c0a52/dqc_reference
[2024-01-24 12:23:05,386] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:23:05,387] [INFO] Task started: Prodigal
[2024-01-24 12:23:05,387] [INFO] Running command: gunzip -c /var/lib/cwl/stg7e8fc09f-aa45-4913-84d0-e4f311a0075d/GCF_016428585.1_ASM1642858v1_genomic.fna.gz | prodigal -d GCF_016428585.1_ASM1642858v1_genomic.fna/cds.fna -a GCF_016428585.1_ASM1642858v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:23:17,460] [INFO] Task succeeded: Prodigal
[2024-01-24 12:23:17,461] [INFO] Task started: HMMsearch
[2024-01-24 12:23:17,461] [INFO] Running command: hmmsearch --tblout GCF_016428585.1_ASM1642858v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc7bfee3a-3304-4d71-8489-ffb5754c0a52/dqc_reference/reference_markers.hmm GCF_016428585.1_ASM1642858v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:23:17,719] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:23:17,721] [INFO] Found 6/6 markers.
[2024-01-24 12:23:17,760] [INFO] Query marker FASTA was written to GCF_016428585.1_ASM1642858v1_genomic.fna/markers.fasta
[2024-01-24 12:23:17,761] [INFO] Task started: Blastn
[2024-01-24 12:23:17,761] [INFO] Running command: blastn -query GCF_016428585.1_ASM1642858v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc7bfee3a-3304-4d71-8489-ffb5754c0a52/dqc_reference/reference_markers.fasta -out GCF_016428585.1_ASM1642858v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:18,691] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:18,697] [INFO] Selected 24 target genomes.
[2024-01-24 12:23:18,697] [INFO] Target genome list was writen to GCF_016428585.1_ASM1642858v1_genomic.fna/target_genomes.txt
[2024-01-24 12:23:18,705] [INFO] Task started: fastANI
[2024-01-24 12:23:18,705] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e8fc09f-aa45-4913-84d0-e4f311a0075d/GCF_016428585.1_ASM1642858v1_genomic.fna.gz --refList GCF_016428585.1_ASM1642858v1_genomic.fna/target_genomes.txt --output GCF_016428585.1_ASM1642858v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:36,941] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:36,942] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc7bfee3a-3304-4d71-8489-ffb5754c0a52/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:36,942] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc7bfee3a-3304-4d71-8489-ffb5754c0a52/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:36,959] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:23:36,960] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:23:36,960] [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
Cribrihabitans marinus	strain=DSM 29340	GCA_900109035.1	1227549	1227549	type	True	79.9737	657	1315	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	79.9109	634	1315	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	79.5804	621	1315	95	below_threshold
Ruegeria sediminis	strain=CAU 1488	GCA_005938215.1	2583820	2583820	type	True	79.5387	586	1315	95	below_threshold
Ruegeria marisrubri	strain=ZGT118	GCA_001507595.1	1685379	1685379	type	True	79.4335	575	1315	95	below_threshold
Ruegeria pomeroyi	strain=DSS-3	GCA_000011965.2	89184	89184	suspected-type	True	79.3812	633	1315	95	below_threshold
Ruegeria intermedia	strain=DSM 29341	GCA_900129345.1	996115	996115	type	True	79.314	573	1315	95	below_threshold
Ruegeria marina	strain=CGMCC 1.9108	GCA_900101475.1	639004	639004	type	True	79.0126	594	1315	95	below_threshold
Leisingera daeponensis	strain=DSM 23529	GCA_000473145.1	405746	405746	type	True	78.8317	524	1315	95	below_threshold
Leisingera aquaemixtae	strain=CECT 8399	GCA_001458395.1	1396826	1396826	type	True	78.7969	512	1315	95	below_threshold
Roseovarius halotolerans	strain=DSM 29507	GCA_003634925.1	505353	505353	type	True	78.6948	461	1315	95	below_threshold
Pontibaca methylaminivorans	strain=DSM 21219	GCA_900156525.1	515897	515897	type	True	78.4843	334	1315	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.4568	421	1315	95	below_threshold
Pelagivirga sediminicola	strain=BH-SD19	GCA_003072125.1	2170575	2170575	type	True	78.3466	410	1315	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	78.2447	446	1315	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	78.1429	467	1315	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	78.1392	459	1315	95	below_threshold
Pseudooceanicola aestuarii	strain=E2-1	GCA_010614805.1	2697319	2697319	type	True	78.1082	391	1315	95	below_threshold
Leisingera aquimarina	strain=DSM 24565	GCA_000473165.1	476529	476529	type	True	78.0941	457	1315	95	below_threshold
Puniceibacterium confluentis	strain=JSSK-17	GCA_007923445.1	1958944	1958944	type	True	78.0412	416	1315	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	77.9342	354	1315	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	77.9338	347	1315	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.7597	338	1315	95	below_threshold
Phaeobacter marinintestinus	strain=UB-M7	GCA_007923355.1	1492905	1492905	type	True	77.4591	423	1315	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:36,962] [INFO] DFAST Taxonomy check result was written to GCF_016428585.1_ASM1642858v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:36,963] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:36,963] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:36,963] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc7bfee3a-3304-4d71-8489-ffb5754c0a52/dqc_reference/checkm_data
[2024-01-24 12:23:36,964] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:37,008] [INFO] Task started: CheckM
[2024-01-24 12:23:37,008] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016428585.1_ASM1642858v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016428585.1_ASM1642858v1_genomic.fna/checkm_input GCF_016428585.1_ASM1642858v1_genomic.fna/checkm_result
[2024-01-24 12:24:16,857] [INFO] Task succeeded: CheckM
[2024-01-24 12:24:16,859] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:24:16,882] [INFO] ===== Completeness check finished =====
[2024-01-24 12:24:16,882] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:24:16,883] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016428585.1_ASM1642858v1_genomic.fna/markers.fasta)
[2024-01-24 12:24:16,883] [INFO] Task started: Blastn
[2024-01-24 12:24:16,883] [INFO] Running command: blastn -query GCF_016428585.1_ASM1642858v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc7bfee3a-3304-4d71-8489-ffb5754c0a52/dqc_reference/reference_markers_gtdb.fasta -out GCF_016428585.1_ASM1642858v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:18,310] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:18,315] [INFO] Selected 19 target genomes.
[2024-01-24 12:24:18,315] [INFO] Target genome list was writen to GCF_016428585.1_ASM1642858v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:24:18,332] [INFO] Task started: fastANI
[2024-01-24 12:24:18,333] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e8fc09f-aa45-4913-84d0-e4f311a0075d/GCF_016428585.1_ASM1642858v1_genomic.fna.gz --refList GCF_016428585.1_ASM1642858v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016428585.1_ASM1642858v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:24:35,432] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:35,450] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:24:35,450] [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_016428585.1	s__Sedimentitalea sp016428585	100.0	1314	1315	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sedimentitalea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900109035.1	s__Cribrihabitans marinus	79.9892	655	1315	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cribrihabitans	95.0	100.00	100.00	0.99	0.99	2	-
GCA_003511785.1	s__UBA7951 sp003511785	79.7443	415	1315	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__UBA7951	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004358185.1	s__Antarcticimicrobium luteum	79.6	619	1315	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005938215.1	s__Ruegeria sediminis	79.5397	585	1315	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000473225.1	s__Sedimentitalea nanhaiensis	79.5083	624	1315	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sedimentitalea	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000161775.1	s__Ruegeria lacuscaerulensis	79.4604	546	1315	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	99.98	99.98	1.00	1.00	2	-
GCF_001507595.1	s__Ruegeria marisrubri	79.4509	573	1315	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000011965.2	s__Ruegeria_B pomeroyi	79.3869	632	1315	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_B	95.0	99.97	99.92	0.99	0.98	5	-
GCF_019104745.1	s__CAU-1522 sp019104745	79.279	522	1315	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CAU-1522	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016521575.1	s__Sedimentitalea sp016521575	79.2673	571	1315	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sedimentitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108275.1	s__Jhaorihella thermophila	79.041	571	1315	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jhaorihella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101475.1	s__Ruegeria_B marina	78.9939	597	1315	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000473145.1	s__Leisingera daeponensis	78.8396	523	1315	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	98.26	98.26	0.94	0.94	2	-
GCA_003217735.2	s__Marinibacterium sp003217735	78.8364	591	1315	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinibacterium	95.0	98.81	98.75	0.89	0.89	3	-
GCF_001458395.1	s__Leisingera aquaemixtae	78.8053	510	1315	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	97.55	97.51	0.94	0.92	3	-
GCF_003651245.1	s__Roseovarius spongiae	78.4574	476	1315	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129395.1	s__Ascidiaceihabitans pseudonitzschiae	78.1395	459	1315	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.99	99.97	0.98	0.96	4	-
GCF_007923355.1	s__Phaeobacter_A marinintestinus	77.4525	424	1315	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:24:35,452] [INFO] GTDB search result was written to GCF_016428585.1_ASM1642858v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:24:35,452] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:24:35,457] [INFO] DFAST_QC result json was written to GCF_016428585.1_ASM1642858v1_genomic.fna/dqc_result.json
[2024-01-24 12:24:35,457] [INFO] DFAST_QC completed!
[2024-01-24 12:24:35,457] [INFO] Total running time: 0h1m32s