[2024-01-24 13:17:34,686] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:34,687] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:34,688] [INFO] DQC Reference Directory: /var/lib/cwl/stgc1a6dbb6-3bd9-466c-a581-3423bcea516c/dqc_reference
[2024-01-24 13:17:36,124] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:36,125] [INFO] Task started: Prodigal
[2024-01-24 13:17:36,125] [INFO] Running command: gunzip -c /var/lib/cwl/stgd3f46e49-428b-4f5c-9bdb-27e37a3fc83e/GCF_019966495.1_ASM1996649v1_genomic.fna.gz | prodigal -d GCF_019966495.1_ASM1996649v1_genomic.fna/cds.fna -a GCF_019966495.1_ASM1996649v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:54,103] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:54,103] [INFO] Task started: HMMsearch
[2024-01-24 13:17:54,103] [INFO] Running command: hmmsearch --tblout GCF_019966495.1_ASM1996649v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc1a6dbb6-3bd9-466c-a581-3423bcea516c/dqc_reference/reference_markers.hmm GCF_019966495.1_ASM1996649v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:54,466] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:54,468] [INFO] Found 6/6 markers.
[2024-01-24 13:17:54,525] [INFO] Query marker FASTA was written to GCF_019966495.1_ASM1996649v1_genomic.fna/markers.fasta
[2024-01-24 13:17:54,525] [INFO] Task started: Blastn
[2024-01-24 13:17:54,525] [INFO] Running command: blastn -query GCF_019966495.1_ASM1996649v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc1a6dbb6-3bd9-466c-a581-3423bcea516c/dqc_reference/reference_markers.fasta -out GCF_019966495.1_ASM1996649v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:55,379] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:55,382] [INFO] Selected 25 target genomes.
[2024-01-24 13:17:55,383] [INFO] Target genome list was writen to GCF_019966495.1_ASM1996649v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:55,390] [INFO] Task started: fastANI
[2024-01-24 13:17:55,390] [INFO] Running command: fastANI --query /var/lib/cwl/stgd3f46e49-428b-4f5c-9bdb-27e37a3fc83e/GCF_019966495.1_ASM1996649v1_genomic.fna.gz --refList GCF_019966495.1_ASM1996649v1_genomic.fna/target_genomes.txt --output GCF_019966495.1_ASM1996649v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:15,903] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:15,904] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc1a6dbb6-3bd9-466c-a581-3423bcea516c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:15,904] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc1a6dbb6-3bd9-466c-a581-3423bcea516c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:15,924] [INFO] Found 25 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:18:15,924] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:18:15,924] [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
Tateyamaria pelophila	strain=DSM 17270	GCA_019966495.1	328415	328415	type	True	100.0	1725	1737	95	conclusive
Tateyamaria omphalii	strain=KCTC 12333	GCA_014651375.1	299262	299262	type	True	78.1712	426	1737	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	78.1159	398	1737	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=DSM 26824	GCA_900129395.1	1402135	1402135	type	True	78.0113	403	1737	95	below_threshold
Falsiruegeria mediterranea	strain=CECT 7615	GCA_900302455.1	1280832	1280832	type	True	77.7204	271	1737	95	below_threshold
Sulfitobacter sabulilitoris	strain=HSMS-29	GCA_005887615.1	2562655	2562655	type	True	77.6732	378	1737	95	below_threshold
Falsiruegeria litorea	strain=CECT 7639	GCA_900172225.1	1280831	1280831	type	True	77.5111	245	1737	95	below_threshold
Roseobacter cerasinus	strain=AI77	GCA_009811755.1	2602289	2602289	type	True	77.418	333	1737	95	below_threshold
Sulfitobacter pontiacus	strain=DSM 10014	GCA_900106935.1	60137	60137	type	True	77.4013	297	1737	95	below_threshold
Cribrihabitans marinus	strain=DSM 29340	GCA_900109035.1	1227549	1227549	type	True	77.228	281	1737	95	below_threshold
Cribrihabitans marinus	strain=CGMCC 1.13219	GCA_014640375.1	1227549	1227549	type	True	77.2248	281	1737	95	below_threshold
Aliishimia ponticola	strain=MYP11	GCA_004803475.1	2499833	2499833	type	True	77.2222	298	1737	95	below_threshold
Pseudooctadecabacter jejudonensis	strain=CECT 8397	GCA_900172275.1	1391910	1391910	type	True	77.2045	176	1737	95	below_threshold
Leisingera aquimarina	strain=DSM 24565	GCA_000473165.1	476529	476529	type	True	77.1153	253	1737	95	below_threshold
Phaeobacter marinintestinus	strain=UB-M7	GCA_007923355.1	1492905	1492905	type	True	77.0796	276	1737	95	below_threshold
Sulfitobacter noctilucicola	strain=NB-77	GCA_000622385.1	1342301	1342301	type	True	77.0492	241	1737	95	below_threshold
Pelagivirga dicentrarchi	strain=YLY04	GCA_003316635.1	2250573	2250573	type	True	77.0309	234	1737	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	76.9474	242	1737	95	below_threshold
Salipiger pallidus	strain=CGMCC 1.15762	GCA_014643635.1	1775170	1775170	type	True	76.9465	176	1737	95	below_threshold
Pseudooceanicola algae	strain=Lw-13e	GCA_003590145.2	1537215	1537215	type	True	76.9152	203	1737	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	76.8612	198	1737	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	76.6952	264	1737	95	below_threshold
Tritonibacter litoralis	strain=SM1979	GCA_009496005.1	2662264	2662264	type	True	76.5548	181	1737	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	76.4801	157	1737	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	76.4801	157	1737	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:15,929] [INFO] DFAST Taxonomy check result was written to GCF_019966495.1_ASM1996649v1_genomic.fna/tc_result.tsv
[2024-01-24 13:18:15,929] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:15,930] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:15,930] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc1a6dbb6-3bd9-466c-a581-3423bcea516c/dqc_reference/checkm_data
[2024-01-24 13:18:15,931] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:15,990] [INFO] Task started: CheckM
[2024-01-24 13:18:15,990] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019966495.1_ASM1996649v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019966495.1_ASM1996649v1_genomic.fna/checkm_input GCF_019966495.1_ASM1996649v1_genomic.fna/checkm_result
[2024-01-24 13:19:12,576] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:12,578] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:12,604] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:12,605] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:12,605] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019966495.1_ASM1996649v1_genomic.fna/markers.fasta)
[2024-01-24 13:19:12,606] [INFO] Task started: Blastn
[2024-01-24 13:19:12,606] [INFO] Running command: blastn -query GCF_019966495.1_ASM1996649v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc1a6dbb6-3bd9-466c-a581-3423bcea516c/dqc_reference/reference_markers_gtdb.fasta -out GCF_019966495.1_ASM1996649v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:14,065] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:14,068] [INFO] Selected 24 target genomes.
[2024-01-24 13:19:14,068] [INFO] Target genome list was writen to GCF_019966495.1_ASM1996649v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:14,085] [INFO] Task started: fastANI
[2024-01-24 13:19:14,086] [INFO] Running command: fastANI --query /var/lib/cwl/stgd3f46e49-428b-4f5c-9bdb-27e37a3fc83e/GCF_019966495.1_ASM1996649v1_genomic.fna.gz --refList GCF_019966495.1_ASM1996649v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019966495.1_ASM1996649v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:31,806] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:31,826] [INFO] Found 24 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:19:31,826] [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_000814025.1	s__Tateyamaria sp000814025	78.372	483	1737	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tateyamaria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001969365.1	s__Tateyamaria omphalii_A	78.3512	494	1737	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tateyamaria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007995245.1	s__Tateyamaria sp007995245	78.2494	474	1737	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tateyamaria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014651375.1	s__Tateyamaria omphalii	78.1748	425	1737	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tateyamaria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900143535.1	s__Tateyamaria sp900143535	78.0895	437	1737	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tateyamaria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129395.1	s__Ascidiaceihabitans pseudonitzschiae	78.0111	403	1737	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.99	99.97	0.98	0.96	4	-
GCF_002222635.1	s__Ascidiaceihabitans pseudonitzschiae_A	78.0	364	1737	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	99.92	99.92	0.96	0.96	2	-
GCF_000620505.1	s__Ascidiaceihabitans sp000620505	77.859	431	1737	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005887615.1	s__Sulfitobacter_E sabulilitoris	77.6835	376	1737	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017854855.1	s__Sulfitobacter sp017854855	77.4887	298	1737	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003352065.1	s__Sulfitobacter sp003352065	77.4536	267	1737	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001650875.1	s__Sulfitobacter sp001650875	77.4516	356	1737	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009811755.1	s__Roseobacter cerasinus	77.419	332	1737	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109145.1	s__Marinovum algicola	77.3185	292	1737	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinovum	95.0	99.11	98.22	0.94	0.88	3	-
GCF_009363555.1	s__Sulfitobacter sp009363555	77.2826	322	1737	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001650895.1	s__EhC02 sp001650895	77.249	301	1737	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__EhC02	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000203975.2	s__Leisingera sp000203975	77.2367	243	1737	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	98.92	98.17	0.96	0.94	6	-
GCF_900109035.1	s__Cribrihabitans marinus	77.228	281	1737	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cribrihabitans	95.0	100.00	100.00	0.99	0.99	2	-
GCF_004803475.1	s__Aliishimia ponticola	77.2228	298	1737	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Aliishimia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001886735.1	s__Sulfitobacter alexandrii	77.1932	287	1737	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018668195.1	s__Tateyamaria sp018668195	77.192	244	1737	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tateyamaria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000473165.1	s__Leisingera aquimarina	77.1045	254	1737	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Leisingera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000220565.1	s__Pseudooceanicola sp000220565	76.9838	169	1737	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003590145.2	s__Pseudooceanicola algae	76.8587	201	1737	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:19:31,828] [INFO] GTDB search result was written to GCF_019966495.1_ASM1996649v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:31,829] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:31,833] [INFO] DFAST_QC result json was written to GCF_019966495.1_ASM1996649v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:31,834] [INFO] DFAST_QC completed!
[2024-01-24 13:19:31,834] [INFO] Total running time: 0h1m57s