[2023-06-27 00:13:11,326] [INFO] DFAST_QC pipeline started.
[2023-06-27 00:13:11,329] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 00:13:11,330] [INFO] DQC Reference Directory: /var/lib/cwl/stg7b82b801-2703-4d08-b76f-0888b63bf32e/dqc_reference
[2023-06-27 00:13:13,028] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 00:13:13,031] [INFO] Task started: Prodigal
[2023-06-27 00:13:13,031] [INFO] Running command: gunzip -c /var/lib/cwl/stg79fa9307-4ab6-490a-bd14-e2d4c59da779/GCA_026419405.1_ASM2641940v1_genomic.fna.gz | prodigal -d GCA_026419405.1_ASM2641940v1_genomic.fna/cds.fna -a GCA_026419405.1_ASM2641940v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 00:13:21,616] [INFO] Task succeeded: Prodigal
[2023-06-27 00:13:21,616] [INFO] Task started: HMMsearch
[2023-06-27 00:13:21,616] [INFO] Running command: hmmsearch --tblout GCA_026419405.1_ASM2641940v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7b82b801-2703-4d08-b76f-0888b63bf32e/dqc_reference/reference_markers.hmm GCA_026419405.1_ASM2641940v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 00:13:21,933] [INFO] Task succeeded: HMMsearch
[2023-06-27 00:13:21,935] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg79fa9307-4ab6-490a-bd14-e2d4c59da779/GCA_026419405.1_ASM2641940v1_genomic.fna.gz]
[2023-06-27 00:13:22,008] [INFO] Query marker FASTA was written to GCA_026419405.1_ASM2641940v1_genomic.fna/markers.fasta
[2023-06-27 00:13:22,008] [INFO] Task started: Blastn
[2023-06-27 00:13:22,008] [INFO] Running command: blastn -query GCA_026419405.1_ASM2641940v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b82b801-2703-4d08-b76f-0888b63bf32e/dqc_reference/reference_markers.fasta -out GCA_026419405.1_ASM2641940v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 00:13:23,034] [INFO] Task succeeded: Blastn
[2023-06-27 00:13:23,039] [INFO] Selected 27 target genomes.
[2023-06-27 00:13:23,040] [INFO] Target genome list was writen to GCA_026419405.1_ASM2641940v1_genomic.fna/target_genomes.txt
[2023-06-27 00:13:23,056] [INFO] Task started: fastANI
[2023-06-27 00:13:23,056] [INFO] Running command: fastANI --query /var/lib/cwl/stg79fa9307-4ab6-490a-bd14-e2d4c59da779/GCA_026419405.1_ASM2641940v1_genomic.fna.gz --refList GCA_026419405.1_ASM2641940v1_genomic.fna/target_genomes.txt --output GCA_026419405.1_ASM2641940v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 00:13:46,304] [INFO] Task succeeded: fastANI
[2023-06-27 00:13:46,304] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7b82b801-2703-4d08-b76f-0888b63bf32e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 00:13:46,305] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7b82b801-2703-4d08-b76f-0888b63bf32e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 00:13:46,325] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 00:13:46,325] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 00:13:46,325] [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
Limimaricola pyoseonensis	strain=DSM 21424	GCA_900102015.1	521013	521013	type	True	79.9705	565	1102	95	below_threshold
Cereibacter azotoformans	strain=KA25	GCA_003050905.1	43057	43057	type	True	79.5406	524	1102	95	below_threshold
Cereibacter sediminicola	strain=JA983	GCA_007668225.1	2584941	2584941	type	True	79.3948	531	1102	95	below_threshold
Rhodobacter calidifons	strain=M37P	GCA_011174775.1	2715277	2715277	type	True	79.2526	532	1102	95	below_threshold
Rhodobacter thermarum	strain=YIM 73036	GCA_003574395.1	2670345	2670345	type	True	79.1143	482	1102	95	below_threshold
Wenxinia marina	strain=DSM 24838	GCA_000379485.1	390641	390641	type	True	79.1063	582	1102	95	below_threshold
Wenxinia marina	strain=DSM 24838	GCA_000836695.1	390641	390641	type	True	79.0613	579	1102	95	below_threshold
Wenxinia marina	strain=CGMCC 1.6105	GCA_014645075.1	390641	390641	type	True	79.0541	591	1102	95	below_threshold
Rhodovulum euryhalinum	strain=DSM 4868	GCA_004342445.1	35805	35805	type	True	79.0369	511	1102	95	below_threshold
Roseivivax isoporae	strain=LMG 25204	GCA_000521865.1	591206	591206	type	True	79.019	590	1102	95	below_threshold
Paracoccus sanguinis	strain=DSM 29303	GCA_900106665.1	1545044	1545044	type	True	78.9006	511	1102	95	below_threshold
Sinirhodobacter huangdaonensis	strain=CGMCC 1.12963	GCA_004022465.1	2501515	2501515	type	True	78.8538	558	1102	95	below_threshold
Rhodovulum robiginosum	strain=DSM 12329	GCA_003944755.1	68292	68292	type	True	78.7001	530	1102	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	78.6659	482	1102	95	below_threshold
Paracoccus solventivorans	strain=DSM 6637	GCA_900142875.1	53463	53463	type	True	78.4988	379	1102	95	below_threshold
Defluviimonas aquaemixtae	strain=CECT 8626	GCA_900302475.1	1542388	1542388	type	True	78.4932	448	1102	95	below_threshold
Pseudoroseicyclus aestuarii	strain=CECT 9025	GCA_003217255.1	1795041	1795041	type	True	78.4504	434	1102	95	below_threshold
Frigidibacter mobilis	strain=cai42	GCA_001620265.1	1335048	1335048	type	True	78.4497	516	1102	95	below_threshold
Rhodovulum strictum	strain=DSM 11289	GCA_009649175.1	58314	58314	type	True	78.406	465	1102	95	below_threshold
Silicimonas algicola	strain=DSM 103371	GCA_003148765.1	1826607	1826607	type	True	78.3859	424	1102	95	below_threshold
Paracoccus sphaerophysae	strain=HAMBI 3106	GCA_000763805.1	690417	690417	type	True	78.2713	428	1102	95	below_threshold
Brevirhabdus pacifica	strain=22DY15	GCA_002094875.1	1267768	1267768	type	True	78.1511	350	1102	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	78.0966	408	1102	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	78.0159	414	1102	95	below_threshold
Brevirhabdus pacifica	strain=DSM 27767	GCA_002797755.1	1267768	1267768	type	True	77.973	398	1102	95	below_threshold
Leisingera aquaemixtae	strain=CECT 8399	GCA_001458395.1	1396826	1396826	type	True	77.3884	380	1102	95	below_threshold
Leisingera daeponensis	strain=DSM 23529	GCA_000473145.1	405746	405746	type	True	77.3659	376	1102	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 00:13:46,332] [INFO] DFAST Taxonomy check result was written to GCA_026419405.1_ASM2641940v1_genomic.fna/tc_result.tsv
[2023-06-27 00:13:46,333] [INFO] ===== Taxonomy check completed =====
[2023-06-27 00:13:46,333] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 00:13:46,333] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7b82b801-2703-4d08-b76f-0888b63bf32e/dqc_reference/checkm_data
[2023-06-27 00:13:46,334] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 00:13:46,378] [INFO] Task started: CheckM
[2023-06-27 00:13:46,378] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026419405.1_ASM2641940v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026419405.1_ASM2641940v1_genomic.fna/checkm_input GCA_026419405.1_ASM2641940v1_genomic.fna/checkm_result
[2023-06-27 00:14:28,100] [INFO] Task succeeded: CheckM
[2023-06-27 00:14:28,101] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 00:14:28,124] [INFO] ===== Completeness check finished =====
[2023-06-27 00:14:28,124] [INFO] ===== Start GTDB Search =====
[2023-06-27 00:14:28,125] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026419405.1_ASM2641940v1_genomic.fna/markers.fasta)
[2023-06-27 00:14:28,125] [INFO] Task started: Blastn
[2023-06-27 00:14:28,125] [INFO] Running command: blastn -query GCA_026419405.1_ASM2641940v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b82b801-2703-4d08-b76f-0888b63bf32e/dqc_reference/reference_markers_gtdb.fasta -out GCA_026419405.1_ASM2641940v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 00:14:30,002] [INFO] Task succeeded: Blastn
[2023-06-27 00:14:30,009] [INFO] Selected 30 target genomes.
[2023-06-27 00:14:30,009] [INFO] Target genome list was writen to GCA_026419405.1_ASM2641940v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 00:14:30,037] [INFO] Task started: fastANI
[2023-06-27 00:14:30,038] [INFO] Running command: fastANI --query /var/lib/cwl/stg79fa9307-4ab6-490a-bd14-e2d4c59da779/GCA_026419405.1_ASM2641940v1_genomic.fna.gz --refList GCA_026419405.1_ASM2641940v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026419405.1_ASM2641940v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 00:14:53,425] [INFO] Task succeeded: fastANI
[2023-06-27 00:14:53,458] [INFO] Found 30 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 00:14:53,459] [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
GCA_011046725.1	s__DSPG01 sp011046725	80.473	587	1102	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__DSPG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008933605.1	s__Albidovulum sp008933605	79.919	505	1102	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albidovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102015.1	s__Limimaricola pyoseonensis	79.9046	572	1102	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012395815.1	s__Roseicyclus sp012395815	79.686	616	1102	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011620265.1	s__Albidovulum sp011620265	79.5933	558	1102	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albidovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003298775.1	s__Rhodosalinus sp003298775	79.3548	550	1102	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodosalinus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007131945.1	s__Pararhodobacter sp007131945	79.3313	425	1102	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pararhodobacter	95.0	99.16	99.15	0.86	0.82	3	-
GCA_002280515.1	s__Albidovulum sp002280515	79.2901	520	1102	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albidovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002869745.1	s__Oceaniglobus roseus	79.252	611	1102	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceaniglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153305.1	s__Oceanicola granulosus	79.2432	570	1102	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002841115.1	s__Albidovulum sp002841115	79.1493	540	1102	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albidovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000379485.1	s__Wenxinia marina	79.1058	583	1102	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Wenxinia	95.0	99.99	99.99	0.99	0.99	3	-
GCA_015689745.1	s__Roseicyclus sp015689745	79.0555	499	1102	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseicyclus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004010155.1	s__Solirhodobacter olei	79.0438	507	1102	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Solirhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004342445.1	s__Rhodovulum euryhalinum	79.0319	511	1102	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018240425.1	s__TMP-24 sp018240425	79.0191	496	1102	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__TMP-24	95.0	99.95	99.95	0.97	0.97	2	-
GCA_001314685.1	s__HLUCCA09 sp001314685	79.0099	536	1102	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__HLUCCA09	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000442255.1	s__Salipiger mucosus	79.0071	570	1102	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003340565.1	s__HLUCCA09 sp003340565	78.9997	594	1102	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__HLUCCA09	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003993775.1	s__Frigidibacter sp003993775	78.8268	551	1102	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Frigidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003944755.1	s__Rhodovulum robiginosum	78.7152	528	1102	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001633165.1	s__Rhodovulum sulfidophilum	78.5359	466	1102	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodovulum	95.0	97.78	97.16	0.92	0.88	14	-
GCF_900302475.1	s__Albidovulum aquaemixtae	78.4999	445	1102	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Albidovulum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001620265.1	s__Frigidibacter mobilis	78.4499	516	1102	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Frigidibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109035.1	s__Cribrihabitans marinus	78.4225	463	1102	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Cribrihabitans	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003789055.1	s__Oceanicola lentulus	78.3788	515	1102	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003241785.1	s__Amaricoccus sp003241785	78.275	521	1102	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Amaricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002280405.1	s__Tabrizicola sp002280405	78.1562	356	1102	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tabrizicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797755.1	s__Brevirhabdus pacifica	77.9908	396	1102	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Brevirhabdus	95.0	99.99	99.97	0.99	0.98	4	-
GCA_003550665.1	s__Rhodobaculum sp003550665	77.9842	362	1102	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobaculum	95.0	99.32	99.19	0.86	0.85	4	-
--------------------------------------------------------------------------------
[2023-06-27 00:14:53,473] [INFO] GTDB search result was written to GCA_026419405.1_ASM2641940v1_genomic.fna/result_gtdb.tsv
[2023-06-27 00:14:53,474] [INFO] ===== GTDB Search completed =====
[2023-06-27 00:14:53,488] [INFO] DFAST_QC result json was written to GCA_026419405.1_ASM2641940v1_genomic.fna/dqc_result.json
[2023-06-27 00:14:53,488] [INFO] DFAST_QC completed!
[2023-06-27 00:14:53,488] [INFO] Total running time: 0h1m42s