[2024-01-25 19:09:20,537] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:09:20,538] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:09:20,538] [INFO] DQC Reference Directory: /var/lib/cwl/stg9e90a484-fe43-43ac-af0a-4f36880d22fb/dqc_reference
[2024-01-25 19:09:21,684] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:09:21,685] [INFO] Task started: Prodigal
[2024-01-25 19:09:21,685] [INFO] Running command: gunzip -c /var/lib/cwl/stg65c3ff4e-5622-47fa-bc1f-4064a3975b7f/GCF_003313245.1_ASM331324v1_genomic.fna.gz | prodigal -d GCF_003313245.1_ASM331324v1_genomic.fna/cds.fna -a GCF_003313245.1_ASM331324v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:09:33,087] [INFO] Task succeeded: Prodigal
[2024-01-25 19:09:33,087] [INFO] Task started: HMMsearch
[2024-01-25 19:09:33,087] [INFO] Running command: hmmsearch --tblout GCF_003313245.1_ASM331324v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9e90a484-fe43-43ac-af0a-4f36880d22fb/dqc_reference/reference_markers.hmm GCF_003313245.1_ASM331324v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:09:33,341] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:09:33,343] [INFO] Found 6/6 markers.
[2024-01-25 19:09:33,376] [INFO] Query marker FASTA was written to GCF_003313245.1_ASM331324v1_genomic.fna/markers.fasta
[2024-01-25 19:09:33,376] [INFO] Task started: Blastn
[2024-01-25 19:09:33,377] [INFO] Running command: blastn -query GCF_003313245.1_ASM331324v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9e90a484-fe43-43ac-af0a-4f36880d22fb/dqc_reference/reference_markers.fasta -out GCF_003313245.1_ASM331324v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:09:34,276] [INFO] Task succeeded: Blastn
[2024-01-25 19:09:34,279] [INFO] Selected 23 target genomes.
[2024-01-25 19:09:34,280] [INFO] Target genome list was writen to GCF_003313245.1_ASM331324v1_genomic.fna/target_genomes.txt
[2024-01-25 19:09:34,302] [INFO] Task started: fastANI
[2024-01-25 19:09:34,302] [INFO] Running command: fastANI --query /var/lib/cwl/stg65c3ff4e-5622-47fa-bc1f-4064a3975b7f/GCF_003313245.1_ASM331324v1_genomic.fna.gz --refList GCF_003313245.1_ASM331324v1_genomic.fna/target_genomes.txt --output GCF_003313245.1_ASM331324v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:09:51,857] [INFO] Task succeeded: fastANI
[2024-01-25 19:09:51,857] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9e90a484-fe43-43ac-af0a-4f36880d22fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:09:51,857] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9e90a484-fe43-43ac-af0a-4f36880d22fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:09:51,871] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:09:51,871] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:09:51,871] [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
Primorskyibacter marinus	strain=PX7	GCA_003313245.1	1977320	1977320	type	True	100.0	1314	1327	95	conclusive
Primorskyibacter sedentarius	strain=DSM 104836	GCA_004342065.1	745311	745311	type	True	82.1791	782	1327	95	below_threshold
Roseovarius pacificus	strain=DSM 29589	GCA_900142665.1	337701	337701	type	True	78.4372	385	1327	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	78.4316	467	1327	95	below_threshold
Roseovarius pacificus	strain=CGMCC 1.7083	GCA_014645335.1	337701	337701	type	True	78.3756	385	1327	95	below_threshold
Marivita lacus	strain=CGMCC 1.12478	GCA_014637725.1	1323742	1323742	type	True	78.3303	402	1327	95	below_threshold
Cribrihabitans marinus	strain=DSM 29340	GCA_900109035.1	1227549	1227549	type	True	78.2811	390	1327	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	78.2573	385	1327	95	below_threshold
Pelagivirga sediminicola	strain=BH-SD19	GCA_003072125.1	2170575	2170575	type	True	78.2489	389	1327	95	below_threshold
Salipiger aestuarii	strain=AD8	GCA_008930655.1	568098	568098	type	True	78.1915	369	1327	95	below_threshold
Salipiger aestuarii	strain=DSM 22011	GCA_003259905.1	568098	568098	type	True	78.123	373	1327	95	below_threshold
Roseivivax lentus	strain=DSM 29430	GCA_900156805.1	633194	633194	type	True	78.0565	366	1327	95	below_threshold
Pseudoprimorskyibacter insulae	strain=CECT 8871	GCA_900302505.1	1695997	1695997	type	True	77.9507	362	1327	95	below_threshold
Ruegeria marina	strain=CGMCC 1.9108	GCA_900101475.1	639004	639004	type	True	77.8881	344	1327	95	below_threshold
Pseudooceanicola antarcticus	strain=Ar-45	GCA_002786285.1	1247613	1247613	type	True	77.7614	292	1327	95	below_threshold
Rhodovulum strictum	strain=DSM 11289	GCA_009649175.1	58314	58314	type	True	77.6817	340	1327	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.6327	300	1327	95	below_threshold
Pseudooceanicola antarcticus	strain=CGMCC 1.12662	GCA_900215355.1	1247613	1247613	type	True	77.6023	291	1327	95	below_threshold
Poseidonocella pacifica	strain=DSM 29316	GCA_900111875.1	871651	871651	type	True	77.5447	226	1327	95	below_threshold
Sagittula marina	strain=DSM 102235	GCA_014196795.1	943940	943940	type	True	77.5303	287	1327	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	77.4643	283	1327	95	below_threshold
Rhabdonatronobacter sediminivivens	strain=IM2376	GCA_013415485.1	2743469	2743469	type	True	77.2699	238	1327	95	below_threshold
Rhodobacter ruber	strain=CCP-1	GCA_009908315.1	1985673	1985673	type	True	77.0248	274	1327	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:09:51,872] [INFO] DFAST Taxonomy check result was written to GCF_003313245.1_ASM331324v1_genomic.fna/tc_result.tsv
[2024-01-25 19:09:51,874] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:09:51,874] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:09:51,874] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9e90a484-fe43-43ac-af0a-4f36880d22fb/dqc_reference/checkm_data
[2024-01-25 19:09:51,875] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:09:51,917] [INFO] Task started: CheckM
[2024-01-25 19:09:51,918] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003313245.1_ASM331324v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003313245.1_ASM331324v1_genomic.fna/checkm_input GCF_003313245.1_ASM331324v1_genomic.fna/checkm_result
[2024-01-25 19:10:28,845] [INFO] Task succeeded: CheckM
[2024-01-25 19:10:28,846] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:10:28,861] [INFO] ===== Completeness check finished =====
[2024-01-25 19:10:28,861] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:10:28,862] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003313245.1_ASM331324v1_genomic.fna/markers.fasta)
[2024-01-25 19:10:28,863] [INFO] Task started: Blastn
[2024-01-25 19:10:28,863] [INFO] Running command: blastn -query GCF_003313245.1_ASM331324v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9e90a484-fe43-43ac-af0a-4f36880d22fb/dqc_reference/reference_markers_gtdb.fasta -out GCF_003313245.1_ASM331324v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:10:30,575] [INFO] Task succeeded: Blastn
[2024-01-25 19:10:30,578] [INFO] Selected 15 target genomes.
[2024-01-25 19:10:30,578] [INFO] Target genome list was writen to GCF_003313245.1_ASM331324v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:10:30,593] [INFO] Task started: fastANI
[2024-01-25 19:10:30,594] [INFO] Running command: fastANI --query /var/lib/cwl/stg65c3ff4e-5622-47fa-bc1f-4064a3975b7f/GCF_003313245.1_ASM331324v1_genomic.fna.gz --refList GCF_003313245.1_ASM331324v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003313245.1_ASM331324v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:10:44,337] [INFO] Task succeeded: fastANI
[2024-01-25 19:10:44,346] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:10:44,346] [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_003313245.1	s__Primorskyibacter marinus	100.0	1316	1327	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Primorskyibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900176485.1	s__Primorskyibacter flagellatus_A	93.7177	1135	1327	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Primorskyibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004342065.1	s__Primorskyibacter sedentarius	82.187	781	1327	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Primorskyibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006226775.1	s__Marinovum sp006226775	78.5622	482	1327	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinovum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014637725.1	s__Marivita lacus	78.3303	402	1327	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017311415.1	s__Salipiger abyssi_A	78.3189	431	1327	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019104745.1	s__CAU-1522 sp019104745	78.2699	433	1327	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CAU-1522	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003072125.1	s__Roseovarius sediminicola	78.2406	390	1327	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259905.1	s__Salipiger aestuarii	78.1038	375	1327	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	99.58	99.38	0.94	0.92	5	-
GCF_900156805.1	s__Roseivivax lentus	78.086	363	1327	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001038505.1	s__Puniceibacterium sp001038505	77.9904	368	1327	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Puniceibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101475.1	s__Ruegeria_B marina	77.8881	344	1327	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_900215355.1	s__Pseudooceanicola antarcticus	77.5757	295	1327	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900111875.1	s__Poseidonocella pacifica	77.5491	227	1327	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Poseidonocella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000220565.1	s__Pseudooceanicola sp000220565	77.5344	301	1327	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:10:44,348] [INFO] GTDB search result was written to GCF_003313245.1_ASM331324v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:10:44,348] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:10:44,352] [INFO] DFAST_QC result json was written to GCF_003313245.1_ASM331324v1_genomic.fna/dqc_result.json
[2024-01-25 19:10:44,352] [INFO] DFAST_QC completed!
[2024-01-25 19:10:44,352] [INFO] Total running time: 0h1m24s