[2024-01-24 12:22:13,101] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:22:13,104] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:22:13,104] [INFO] DQC Reference Directory: /var/lib/cwl/stg52090e1d-6b5b-4c37-9268-77c5027bfefb/dqc_reference
[2024-01-24 12:22:14,467] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:22:14,468] [INFO] Task started: Prodigal
[2024-01-24 12:22:14,468] [INFO] Running command: gunzip -c /var/lib/cwl/stg4467cfaa-7b69-450a-b557-9f4a8b710a60/GCF_019798055.1_AS10_genomic.fna.gz | prodigal -d GCF_019798055.1_AS10_genomic.fna/cds.fna -a GCF_019798055.1_AS10_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:32,965] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:32,965] [INFO] Task started: HMMsearch
[2024-01-24 12:22:32,965] [INFO] Running command: hmmsearch --tblout GCF_019798055.1_AS10_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg52090e1d-6b5b-4c37-9268-77c5027bfefb/dqc_reference/reference_markers.hmm GCF_019798055.1_AS10_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:33,413] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:33,414] [INFO] Found 6/6 markers.
[2024-01-24 12:22:33,493] [INFO] Query marker FASTA was written to GCF_019798055.1_AS10_genomic.fna/markers.fasta
[2024-01-24 12:22:33,493] [INFO] Task started: Blastn
[2024-01-24 12:22:33,494] [INFO] Running command: blastn -query GCF_019798055.1_AS10_genomic.fna/markers.fasta -db /var/lib/cwl/stg52090e1d-6b5b-4c37-9268-77c5027bfefb/dqc_reference/reference_markers.fasta -out GCF_019798055.1_AS10_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:34,393] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:34,398] [INFO] Selected 21 target genomes.
[2024-01-24 12:22:34,398] [INFO] Target genome list was writen to GCF_019798055.1_AS10_genomic.fna/target_genomes.txt
[2024-01-24 12:22:34,407] [INFO] Task started: fastANI
[2024-01-24 12:22:34,407] [INFO] Running command: fastANI --query /var/lib/cwl/stg4467cfaa-7b69-450a-b557-9f4a8b710a60/GCF_019798055.1_AS10_genomic.fna.gz --refList GCF_019798055.1_AS10_genomic.fna/target_genomes.txt --output GCF_019798055.1_AS10_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:56,079] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:56,079] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg52090e1d-6b5b-4c37-9268-77c5027bfefb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:56,080] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg52090e1d-6b5b-4c37-9268-77c5027bfefb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:56,097] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:22:56,098] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:22:56,098] [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
Salsipaludibacter albus	strain=AS10	GCA_019798055.1	2849650	2849650	type	True	100.0	1378	1381	95	conclusive
Egicoccus halophilus	strain=EGI 80432	GCA_004300825.1	1670830	1670830	type	True	77.1804	384	1381	95	below_threshold
Egicoccus halophilus	strain=CGMCC 1.14988	GCA_014640475.1	1670830	1670830	type	True	77.1274	380	1381	95	below_threshold
Nitriliruptor alkaliphilus	strain=DSM 45188	GCA_000969705.1	427918	427918	type	True	76.9838	398	1381	95	below_threshold
Euzebya rosea	strain=DSW09	GCA_003073135.1	2052804	2052804	type	True	76.068	319	1381	95	below_threshold
Euzebya pacifica	strain=DY32-46	GCA_003344865.1	1608957	1608957	type	True	76.0188	320	1381	95	below_threshold
Egibacter rhizosphaerae	strain=EGI 80759	GCA_004322855.1	1670831	1670831	type	True	75.5175	206	1381	95	below_threshold
Phycicoccus flavus	strain=CMS6Z-2	GCA_004025965.2	2502783	2502783	type	True	75.4833	265	1381	95	below_threshold
Citricoccus zhacaiensis	strain=CGMCC 1.7064	GCA_014645315.1	489142	489142	type	True	75.349	84	1381	95	below_threshold
Desertihabitans brevis	strain=16Sb5-5	GCA_003327535.1	2268447	2268447	type	True	75.3456	247	1381	95	below_threshold
Amycolatopsis lexingtonensis	strain=DSM 44653	GCA_014873755.1	218822	218822	type	True	75.2128	380	1381	95	below_threshold
Amycolatopsis eburnea	strain=GLM-1	GCA_003937945.1	2267691	2267691	type	True	75.1936	366	1381	95	below_threshold
Amycolatopsis arida	strain=DSM 45648	GCA_004365925.1	587909	587909	type	True	75.1803	277	1381	95	below_threshold
Amycolatopsis anabasis	strain=EGI 650086	GCA_009765355.1	1840409	1840409	type	True	75.1741	262	1381	95	below_threshold
Amycolatopsis arida	strain=CGMCC 4.5579	GCA_900115565.1	587909	587909	type	True	75.17	272	1381	95	below_threshold
Amycolatopsis lexingtonensis	strain=NRRL B-24131	GCA_002156005.1	218822	218822	type	True	75.1421	347	1381	95	below_threshold
Thioflavicoccus mobilis	strain=8321	GCA_000327045.1	80679	80679	type	True	75.0113	73	1381	95	below_threshold
Actinomadura spongiicola	strain=LHW52907	GCA_003432485.1	2303421	2303421	type	True	75.003	246	1381	95	below_threshold
Sulfurifustis variabilis	strain=skN76	GCA_002355415.1	1675686	1675686	type	True	74.9247	70	1381	95	below_threshold
Methylobacterium tarhaniae	strain=DSM 25844	GCA_001043955.1	1187852	1187852	type	True	74.7645	171	1381	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:56,100] [INFO] DFAST Taxonomy check result was written to GCF_019798055.1_AS10_genomic.fna/tc_result.tsv
[2024-01-24 12:22:56,101] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:56,101] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:56,101] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg52090e1d-6b5b-4c37-9268-77c5027bfefb/dqc_reference/checkm_data
[2024-01-24 12:22:56,103] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:56,145] [INFO] Task started: CheckM
[2024-01-24 12:22:56,145] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019798055.1_AS10_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019798055.1_AS10_genomic.fna/checkm_input GCF_019798055.1_AS10_genomic.fna/checkm_result
[2024-01-24 12:24:13,740] [INFO] Task succeeded: CheckM
[2024-01-24 12:24:13,741] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:24:13,769] [INFO] ===== Completeness check finished =====
[2024-01-24 12:24:13,770] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:24:13,770] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019798055.1_AS10_genomic.fna/markers.fasta)
[2024-01-24 12:24:13,771] [INFO] Task started: Blastn
[2024-01-24 12:24:13,771] [INFO] Running command: blastn -query GCF_019798055.1_AS10_genomic.fna/markers.fasta -db /var/lib/cwl/stg52090e1d-6b5b-4c37-9268-77c5027bfefb/dqc_reference/reference_markers_gtdb.fasta -out GCF_019798055.1_AS10_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:15,077] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:15,081] [INFO] Selected 22 target genomes.
[2024-01-24 12:24:15,082] [INFO] Target genome list was writen to GCF_019798055.1_AS10_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:24:15,116] [INFO] Task started: fastANI
[2024-01-24 12:24:15,116] [INFO] Running command: fastANI --query /var/lib/cwl/stg4467cfaa-7b69-450a-b557-9f4a8b710a60/GCF_019798055.1_AS10_genomic.fna.gz --refList GCF_019798055.1_AS10_genomic.fna/target_genomes_gtdb.txt --output GCF_019798055.1_AS10_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:24:32,189] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:32,212] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:24:32,212] [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_004300825.1	s__Egicoccus halophilus	77.2464	375	1381	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nitriliruptorales;f__Nitriliruptoraceae;g__Egicoccus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000969705.1	s__Nitriliruptor alkaliphilus	76.9947	396	1381	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nitriliruptorales;f__Nitriliruptoraceae;g__Nitriliruptor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007123425.1	s__SKLC01 sp007123425	76.9805	221	1381	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nitriliruptorales;f__Nitriliruptoraceae;g__SKLC01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007133465.1	s__SLMP01 sp007133465	76.8689	259	1381	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nitriliruptorales;f__Nitriliruptoraceae;g__SLMP01	95.0	99.22	99.05	0.81	0.81	3	-
GCA_007120465.1	s__CSSed11-175R1 sp007120465	76.8551	260	1381	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nitriliruptorales;f__Nitriliruptoraceae;g__CSSed11-175R1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007130695.1	s__SKLC01 sp007130695	76.8327	260	1381	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nitriliruptorales;f__Nitriliruptoraceae;g__SKLC01	95.0	99.35	99.35	0.92	0.92	2	-
GCA_003563915.1	s__CSSed11-175R1 sp003563915	76.7918	249	1381	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nitriliruptorales;f__Nitriliruptoraceae;g__CSSed11-175R1	95.0	99.36	99.32	0.88	0.87	4	-
GCA_003558435.1	s__PWLR01 sp003558435	76.7379	275	1381	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nitriliruptorales;f__Nitriliruptoraceae;g__PWLR01	95.0	99.63	99.63	0.94	0.94	2	-
GCA_007118045.1	s__SKTG01 sp007118045	76.6184	260	1381	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nitriliruptorales;f__Nitriliruptoraceae;g__SKTG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003561535.1	s__T1Sed10-7 sp003561535	76.5944	240	1381	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nitriliruptorales;f__Nitriliruptoraceae;g__T1Sed10-7	95.0	98.89	95.80	0.87	0.76	8	-
GCA_003554005.1	s__T1Sed10-7 sp003554005	76.5543	208	1381	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nitriliruptorales;f__Nitriliruptoraceae;g__T1Sed10-7	95.0	98.88	98.67	0.78	0.76	5	-
GCA_007117945.1	s__T1Sed10-7 sp007117945	76.4945	168	1381	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nitriliruptorales;f__Nitriliruptoraceae;g__T1Sed10-7	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007125475.1	s__SLDB01 sp007125475	76.4277	203	1381	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nitriliruptorales;f__Nitriliruptoraceae;g__SLDB01	95.0	98.81	98.81	0.77	0.77	2	-
GCA_007131525.1	s__T1Sed10-7 sp007131525	76.3674	178	1381	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nitriliruptorales;f__Nitriliruptoraceae;g__T1Sed10-7	95.0	98.34	98.34	0.77	0.77	2	-
GCA_007121975.1	s__SKJO01 sp007121975	76.3618	205	1381	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nitriliruptorales;f__Nitriliruptoraceae;g__SKJO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003565155.1	s__T1Sed10-7 sp003565155	76.3215	221	1381	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nitriliruptorales;f__Nitriliruptoraceae;g__T1Sed10-7	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004025965.2	s__Phycicoccus flavus	75.474	267	1381	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008042275.1	s__Streptomyces sp008042275	75.1918	227	1381	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003937945.1	s__Amycolatopsis eburnea	75.189	368	1381	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115565.1	s__Yuhushiella arida	75.176	270	1381	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Yuhushiella	95.0	100.00	100.00	0.99	0.99	2	-
GCF_001983105.1	s__Frankia asymbiotica	75.0985	302	1381	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Frankiaceae;g__Frankia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862395.1	s__Actinoplanes siamensis	75.0544	271	1381	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:24:32,214] [INFO] GTDB search result was written to GCF_019798055.1_AS10_genomic.fna/result_gtdb.tsv
[2024-01-24 12:24:32,214] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:24:32,219] [INFO] DFAST_QC result json was written to GCF_019798055.1_AS10_genomic.fna/dqc_result.json
[2024-01-24 12:24:32,219] [INFO] DFAST_QC completed!
[2024-01-24 12:24:32,219] [INFO] Total running time: 0h2m19s