[2024-01-24 12:23:03,858] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:23:03,860] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:23:03,860] [INFO] DQC Reference Directory: /var/lib/cwl/stgd81b5135-d1f7-4caa-9b78-b16b0a39e3c4/dqc_reference
[2024-01-24 12:23:05,252] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:23:05,254] [INFO] Task started: Prodigal
[2024-01-24 12:23:05,254] [INFO] Running command: gunzip -c /var/lib/cwl/stgcf98d6f2-c1c1-46b9-b79d-b5cb68f594bf/GCF_002094885.1_ASM209488v1_genomic.fna.gz | prodigal -d GCF_002094885.1_ASM209488v1_genomic.fna/cds.fna -a GCF_002094885.1_ASM209488v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:23:13,963] [INFO] Task succeeded: Prodigal
[2024-01-24 12:23:13,963] [INFO] Task started: HMMsearch
[2024-01-24 12:23:13,963] [INFO] Running command: hmmsearch --tblout GCF_002094885.1_ASM209488v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd81b5135-d1f7-4caa-9b78-b16b0a39e3c4/dqc_reference/reference_markers.hmm GCF_002094885.1_ASM209488v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:23:14,201] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:23:14,203] [INFO] Found 6/6 markers.
[2024-01-24 12:23:14,233] [INFO] Query marker FASTA was written to GCF_002094885.1_ASM209488v1_genomic.fna/markers.fasta
[2024-01-24 12:23:14,234] [INFO] Task started: Blastn
[2024-01-24 12:23:14,234] [INFO] Running command: blastn -query GCF_002094885.1_ASM209488v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd81b5135-d1f7-4caa-9b78-b16b0a39e3c4/dqc_reference/reference_markers.fasta -out GCF_002094885.1_ASM209488v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:15,232] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:15,236] [INFO] Selected 25 target genomes.
[2024-01-24 12:23:15,237] [INFO] Target genome list was writen to GCF_002094885.1_ASM209488v1_genomic.fna/target_genomes.txt
[2024-01-24 12:23:15,245] [INFO] Task started: fastANI
[2024-01-24 12:23:15,246] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf98d6f2-c1c1-46b9-b79d-b5cb68f594bf/GCF_002094885.1_ASM209488v1_genomic.fna.gz --refList GCF_002094885.1_ASM209488v1_genomic.fna/target_genomes.txt --output GCF_002094885.1_ASM209488v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:34,254] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:34,255] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd81b5135-d1f7-4caa-9b78-b16b0a39e3c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:34,255] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd81b5135-d1f7-4caa-9b78-b16b0a39e3c4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:34,278] [INFO] Found 25 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:23:34,279] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:23:34,279] [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
Salibaculum halophilum	strain=WDS1C4	GCA_002094885.1	1914408	1914408	type	True	100.0	934	938	95	conclusive
Salibaculum griseiflavum	strain=WDS4C29	GCA_003129565.1	1914409	1914409	type	True	82.5591	704	938	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	79.1091	489	938	95	below_threshold
Salipiger profundus	strain=JLT2016	GCA_001969385.1	1229727	1229727	type	True	78.9952	434	938	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.9681	399	938	95	below_threshold
Mameliella alba	strain=DSM 26384	GCA_003051025.1	561184	561184	suspected-type	True	78.945	454	938	95	below_threshold
Salipiger profundus	strain=CGMCC 1.12377	GCA_014637265.1	1229727	1229727	type	True	78.9058	436	938	95	below_threshold
Rhodovulum robiginosum	strain=DSM 12329	GCA_003944755.1	68292	68292	type	True	78.9003	462	938	95	below_threshold
Roseivivax lentus	strain=DSM 29430	GCA_900156805.1	633194	633194	type	True	78.7206	467	938	95	below_threshold
Roseivivax isoporae	strain=LMG 25204	GCA_000521865.1	591206	591206	type	True	78.6948	464	938	95	below_threshold
Roseovarius nitratireducens	strain=TFZ	GCA_002925845.1	2044597	2044597	type	True	78.656	397	938	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_900112725.1	540747	540747	type	True	78.6338	439	938	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	78.6304	388	938	95	below_threshold
Rhodovulum strictum	strain=DSM 11289	GCA_009649175.1	58314	58314	type	True	78.6286	422	938	95	below_threshold
Roseovarius indicus	strain=B108	GCA_001441635.1	540747	540747	type	True	78.6045	444	938	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	78.5703	375	938	95	below_threshold
Roseovarius indicus	strain=DSM 26383	GCA_008728195.1	540747	540747	type	True	78.5452	449	938	95	below_threshold
Yangia pacifica	strain=DSM 26894	GCA_900116195.1	311180	311180	suspected-type	True	78.4939	451	938	95	below_threshold
Pseudooceanicola antarcticus	strain=Ar-45	GCA_002786285.1	1247613	1247613	type	True	78.4333	422	938	95	below_threshold
Pseudooceanicola antarcticus	strain=CGMCC 1.12662	GCA_900215355.1	1247613	1247613	type	True	78.3929	424	938	95	below_threshold
Pseudooceanicola endophyticus	strain=CBS1P-1	GCA_018760365.1	2841273	2841273	type	True	78.3181	424	938	95	below_threshold
Paracoccus mutanolyticus	strain=RSP-02	GCA_003285265.1	1499308	1499308	type	True	78.1113	323	938	95	below_threshold
Mangrovicoccus algicola	strain=HB182678	GCA_014903745.1	2771008	2771008	type	True	78.0476	378	938	95	below_threshold
Paracoccus shandongensis	strain=wg2	GCA_017315735.1	2816048	2816048	type	True	77.9419	338	938	95	below_threshold
Roseivivax halotolerans	strain=JCM 10271	GCA_900115815.1	93684	93684	type	True	77.7465	326	938	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:34,280] [INFO] DFAST Taxonomy check result was written to GCF_002094885.1_ASM209488v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:34,281] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:34,281] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:34,281] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd81b5135-d1f7-4caa-9b78-b16b0a39e3c4/dqc_reference/checkm_data
[2024-01-24 12:23:34,283] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:34,321] [INFO] Task started: CheckM
[2024-01-24 12:23:34,321] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002094885.1_ASM209488v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002094885.1_ASM209488v1_genomic.fna/checkm_input GCF_002094885.1_ASM209488v1_genomic.fna/checkm_result
[2024-01-24 12:24:04,918] [INFO] Task succeeded: CheckM
[2024-01-24 12:24:04,919] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:24:04,941] [INFO] ===== Completeness check finished =====
[2024-01-24 12:24:04,942] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:24:04,942] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002094885.1_ASM209488v1_genomic.fna/markers.fasta)
[2024-01-24 12:24:04,942] [INFO] Task started: Blastn
[2024-01-24 12:24:04,943] [INFO] Running command: blastn -query GCF_002094885.1_ASM209488v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd81b5135-d1f7-4caa-9b78-b16b0a39e3c4/dqc_reference/reference_markers_gtdb.fasta -out GCF_002094885.1_ASM209488v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:06,645] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:06,650] [INFO] Selected 19 target genomes.
[2024-01-24 12:24:06,650] [INFO] Target genome list was writen to GCF_002094885.1_ASM209488v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:24:06,662] [INFO] Task started: fastANI
[2024-01-24 12:24:06,662] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf98d6f2-c1c1-46b9-b79d-b5cb68f594bf/GCF_002094885.1_ASM209488v1_genomic.fna.gz --refList GCF_002094885.1_ASM209488v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002094885.1_ASM209488v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:24:20,985] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:21,006] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:24:21,007] [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_002094885.1	s__Salibaculum halophilum	100.0	934	938	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salibaculum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_009908505.1	s__Salibaculum sp009908505	83.7769	672	938	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003129565.1	s__Salibaculum griseiflavum	82.5703	703	938	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001314655.1	s__Salibaculum sp001314655	80.0825	581	938	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002166865.1	s__Roseovarius sp002166865	79.7481	470	938	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001482405.1	s__Ponticoccus marisrubri	79.5983	555	938	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ponticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142185.1	s__Lutimaribacter pacificus	79.4869	485	938	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lutimaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_018139985.1	s__JAGSOU01 sp018139985	79.4183	473	938	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__JAGSOU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153305.1	s__Oceanicola granulosus	79.1965	477	938	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001969385.1	s__Salipiger profundus	79.0069	436	938	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	99.85	99.64	0.97	0.94	5	-
GCF_900101505.1	s__Mameliella alba	78.9487	453	938	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Mameliella	95.0	98.60	98.14	0.96	0.94	14	-
GCF_900172235.1	s__Pseudoruegeria aquimaris	78.8353	442	938	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudoruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000521865.1	s__Roseivivax isoporae	78.6996	464	938	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003417655.1	s__Lentibacter sp003417655	78.5949	367	938	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Lentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003122205.1	s__QEYE01 sp003122205	78.4483	390	938	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__QEYE01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018222585.1	s__Pseudooceanicola sp018222585	78.4394	443	938	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.94	99.94	0.96	0.96	2	-
GCA_016278295.1	s__Roseovarius sp016278295	78.4133	330	938	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003072065.1	s__Thalassorhabdomicrobium marinisediminis	78.396	417	938	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassorhabdomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900215355.1	s__Pseudooceanicola antarcticus	78.3923	423	938	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:24:21,008] [INFO] GTDB search result was written to GCF_002094885.1_ASM209488v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:24:21,009] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:24:21,013] [INFO] DFAST_QC result json was written to GCF_002094885.1_ASM209488v1_genomic.fna/dqc_result.json
[2024-01-24 12:24:21,014] [INFO] DFAST_QC completed!
[2024-01-24 12:24:21,014] [INFO] Total running time: 0h1m17s