[2024-01-24 14:15:34,156] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:15:34,158] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:15:34,159] [INFO] DQC Reference Directory: /var/lib/cwl/stg7cb2f1ba-3395-46cd-9a08-9eba747e5a35/dqc_reference
[2024-01-24 14:15:35,547] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:15:35,547] [INFO] Task started: Prodigal
[2024-01-24 14:15:35,548] [INFO] Running command: gunzip -c /var/lib/cwl/stga5b32c5f-3c40-46e3-9b68-7f08b49295ac/GCF_013377785.1_ASM1337778v1_genomic.fna.gz | prodigal -d GCF_013377785.1_ASM1337778v1_genomic.fna/cds.fna -a GCF_013377785.1_ASM1337778v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:15:51,682] [INFO] Task succeeded: Prodigal
[2024-01-24 14:15:51,682] [INFO] Task started: HMMsearch
[2024-01-24 14:15:51,682] [INFO] Running command: hmmsearch --tblout GCF_013377785.1_ASM1337778v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7cb2f1ba-3395-46cd-9a08-9eba747e5a35/dqc_reference/reference_markers.hmm GCF_013377785.1_ASM1337778v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:15:52,031] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:15:52,033] [INFO] Found 6/6 markers.
[2024-01-24 14:15:52,078] [INFO] Query marker FASTA was written to GCF_013377785.1_ASM1337778v1_genomic.fna/markers.fasta
[2024-01-24 14:15:52,078] [INFO] Task started: Blastn
[2024-01-24 14:15:52,078] [INFO] Running command: blastn -query GCF_013377785.1_ASM1337778v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7cb2f1ba-3395-46cd-9a08-9eba747e5a35/dqc_reference/reference_markers.fasta -out GCF_013377785.1_ASM1337778v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:52,882] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:52,885] [INFO] Selected 17 target genomes.
[2024-01-24 14:15:52,885] [INFO] Target genome list was writen to GCF_013377785.1_ASM1337778v1_genomic.fna/target_genomes.txt
[2024-01-24 14:15:52,897] [INFO] Task started: fastANI
[2024-01-24 14:15:52,898] [INFO] Running command: fastANI --query /var/lib/cwl/stga5b32c5f-3c40-46e3-9b68-7f08b49295ac/GCF_013377785.1_ASM1337778v1_genomic.fna.gz --refList GCF_013377785.1_ASM1337778v1_genomic.fna/target_genomes.txt --output GCF_013377785.1_ASM1337778v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:16:08,180] [INFO] Task succeeded: fastANI
[2024-01-24 14:16:08,180] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7cb2f1ba-3395-46cd-9a08-9eba747e5a35/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:16:08,181] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7cb2f1ba-3395-46cd-9a08-9eba747e5a35/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:16:08,194] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:16:08,195] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:16:08,195] [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
Ruegeria haliotis	strain=B1Z28	GCA_013377785.1	2747601	2747601	type	True	100.0	1557	1558	95	conclusive
Ruegeria atlantica	strain=CECT 4292	GCA_001458195.1	81569	81569	suspected-type	True	80.9365	751	1558	95	below_threshold
Ruegeria meonggei	strain=CECT 8411	GCA_900172215.1	1446476	1446476	type	True	80.8755	803	1558	95	below_threshold
Ruegeria halocynthiae	strain=DSM 27839	GCA_900106805.1	985054	985054	type	True	80.8345	731	1558	95	below_threshold
Ruegeria denitrificans	strain=CECT 5091	GCA_001458295.1	1715692	1715692	type	True	80.8088	777	1558	95	below_threshold
Ruegeria intermedia	strain=DSM 29341	GCA_900129345.1	996115	996115	type	True	80.5933	713	1558	95	below_threshold
Ruegeria faecimaris	strain=DSM 28009	GCA_900182615.1	686389	686389	type	True	80.4939	708	1558	95	below_threshold
Ruegeria conchae	strain=DSM 29317	GCA_003664205.1	981384	981384	suspected-type	True	80.3774	668	1558	95	below_threshold
Ruegeria conchae	strain=TW15	GCA_000192475.2	981384	981384	suspected-type	True	80.331	670	1558	95	below_threshold
Ruegeria sediminis	strain=CAU 1488	GCA_005938215.1	2583820	2583820	type	True	79.2645	584	1558	95	below_threshold
Falsiruegeria litorea	strain=CECT 7639	GCA_900172225.1	1280831	1280831	type	True	78.6144	496	1558	95	below_threshold
Leisingera aquimarina	strain=DSM 24565	GCA_000473165.1	476529	476529	type	True	78.2833	400	1558	95	below_threshold
Pseudophaeobacter flagellatus	strain=MA21411-1	GCA_021228235.1	2899119	2899119	type	True	77.532	300	1558	95	below_threshold
Marivivens aquimaris	strain=GSB7	GCA_015220045.1	2774876	2774876	type	True	76.9662	147	1558	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	76.9509	198	1558	95	below_threshold
Celeribacter litoreus	strain=ASW11-22	GCA_020165855.1	2876714	2876714	type	True	76.8339	124	1558	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	76.7118	177	1558	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:16:08,197] [INFO] DFAST Taxonomy check result was written to GCF_013377785.1_ASM1337778v1_genomic.fna/tc_result.tsv
[2024-01-24 14:16:08,197] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:16:08,198] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:16:08,198] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7cb2f1ba-3395-46cd-9a08-9eba747e5a35/dqc_reference/checkm_data
[2024-01-24 14:16:08,199] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:16:08,249] [INFO] Task started: CheckM
[2024-01-24 14:16:08,249] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013377785.1_ASM1337778v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013377785.1_ASM1337778v1_genomic.fna/checkm_input GCF_013377785.1_ASM1337778v1_genomic.fna/checkm_result
[2024-01-24 14:16:56,773] [INFO] Task succeeded: CheckM
[2024-01-24 14:16:56,775] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:16:56,798] [INFO] ===== Completeness check finished =====
[2024-01-24 14:16:56,799] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:16:56,800] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013377785.1_ASM1337778v1_genomic.fna/markers.fasta)
[2024-01-24 14:16:56,800] [INFO] Task started: Blastn
[2024-01-24 14:16:56,800] [INFO] Running command: blastn -query GCF_013377785.1_ASM1337778v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7cb2f1ba-3395-46cd-9a08-9eba747e5a35/dqc_reference/reference_markers_gtdb.fasta -out GCF_013377785.1_ASM1337778v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:16:58,049] [INFO] Task succeeded: Blastn
[2024-01-24 14:16:58,057] [INFO] Selected 19 target genomes.
[2024-01-24 14:16:58,057] [INFO] Target genome list was writen to GCF_013377785.1_ASM1337778v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:16:58,071] [INFO] Task started: fastANI
[2024-01-24 14:16:58,071] [INFO] Running command: fastANI --query /var/lib/cwl/stga5b32c5f-3c40-46e3-9b68-7f08b49295ac/GCF_013377785.1_ASM1337778v1_genomic.fna.gz --refList GCF_013377785.1_ASM1337778v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013377785.1_ASM1337778v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:17:16,169] [INFO] Task succeeded: fastANI
[2024-01-24 14:17:16,190] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:17:16,191] [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_013377785.1	s__Ruegeria haliotis	100.0	1557	1558	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000743705.1	s__Ruegeria halocynthiae_B	81.7002	826	1558	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900313035.1	s__Ruegeria sp900313035	81.6751	912	1558	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013030985.1	s__Ruegeria arenilitoris_B	81.2649	863	1558	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	99.15	99.15	0.92	0.92	2	-
GCF_013031245.1	s__Ruegeria lacuscaerulensis_C	81.1401	819	1558	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013032025.1	s__Ruegeria atlantica_C	81.1209	801	1558	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	100.00	100.00	0.99	0.99	2	-
GCF_013031355.1	s__Ruegeria arenilitoris_C	81.1173	840	1558	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	99.51	99.51	0.98	0.98	2	-
GCF_013033965.1	s__Ruegeria atlantica_D	80.9744	774	1558	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013032005.1	s__Ruegeria atlantica_A	80.9608	793	1558	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	98.11	97.00	0.94	0.90	12	-
GCF_003443535.1	s__Ruegeria sp003443535	80.8921	766	1558	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900172215.1	s__Ruegeria meonggei	80.8755	803	1558	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017743995.1	s__Ruegeria sp017743995	80.7985	772	1558	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000158135.1	s__Ruegeria sp000158135	80.7561	703	1558	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000813985.1	s__Ruegeria sp000813985	80.6076	738	1558	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013030265.1	s__Ruegeria arenilitoris_E	80.5316	736	1558	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900182615.1	s__Ruegeria faecimaris	80.4853	709	1558	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013111185.1	s__Ruegeria sp013111185	80.4609	756	1558	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	98.94	97.94	0.92	0.90	11	-
GCF_000814005.1	s__Ruegeria sp000814005	80.0544	596	1558	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017743935.1	s__Ruegeria_E sp017743935	78.5354	523	1558	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ruegeria_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:17:16,193] [INFO] GTDB search result was written to GCF_013377785.1_ASM1337778v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:17:16,193] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:17:16,197] [INFO] DFAST_QC result json was written to GCF_013377785.1_ASM1337778v1_genomic.fna/dqc_result.json
[2024-01-24 14:17:16,198] [INFO] DFAST_QC completed!
[2024-01-24 14:17:16,198] [INFO] Total running time: 0h1m42s