[2024-01-24 12:29:28,899] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:29:28,902] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:29:28,902] [INFO] DQC Reference Directory: /var/lib/cwl/stg365fc2e9-39ab-4e65-89f2-dac23f818a2d/dqc_reference
[2024-01-24 12:29:30,285] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:29:30,286] [INFO] Task started: Prodigal
[2024-01-24 12:29:30,286] [INFO] Running command: gunzip -c /var/lib/cwl/stg643b560d-955f-4542-a872-5ee72dacfcd9/GCF_003751635.1_ASM375163v1_genomic.fna.gz | prodigal -d GCF_003751635.1_ASM375163v1_genomic.fna/cds.fna -a GCF_003751635.1_ASM375163v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:29:37,800] [INFO] Task succeeded: Prodigal
[2024-01-24 12:29:37,801] [INFO] Task started: HMMsearch
[2024-01-24 12:29:37,801] [INFO] Running command: hmmsearch --tblout GCF_003751635.1_ASM375163v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg365fc2e9-39ab-4e65-89f2-dac23f818a2d/dqc_reference/reference_markers.hmm GCF_003751635.1_ASM375163v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:29:38,125] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:29:38,127] [INFO] Found 6/6 markers.
[2024-01-24 12:29:38,172] [INFO] Query marker FASTA was written to GCF_003751635.1_ASM375163v1_genomic.fna/markers.fasta
[2024-01-24 12:29:38,172] [INFO] Task started: Blastn
[2024-01-24 12:29:38,172] [INFO] Running command: blastn -query GCF_003751635.1_ASM375163v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg365fc2e9-39ab-4e65-89f2-dac23f818a2d/dqc_reference/reference_markers.fasta -out GCF_003751635.1_ASM375163v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:29:39,153] [INFO] Task succeeded: Blastn
[2024-01-24 12:29:39,163] [INFO] Selected 24 target genomes.
[2024-01-24 12:29:39,164] [INFO] Target genome list was writen to GCF_003751635.1_ASM375163v1_genomic.fna/target_genomes.txt
[2024-01-24 12:29:39,184] [INFO] Task started: fastANI
[2024-01-24 12:29:39,184] [INFO] Running command: fastANI --query /var/lib/cwl/stg643b560d-955f-4542-a872-5ee72dacfcd9/GCF_003751635.1_ASM375163v1_genomic.fna.gz --refList GCF_003751635.1_ASM375163v1_genomic.fna/target_genomes.txt --output GCF_003751635.1_ASM375163v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:29:55,791] [INFO] Task succeeded: fastANI
[2024-01-24 12:29:55,791] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg365fc2e9-39ab-4e65-89f2-dac23f818a2d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:29:55,792] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg365fc2e9-39ab-4e65-89f2-dac23f818a2d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:29:55,818] [INFO] Found 24 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:29:55,818] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:29:55,818] [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
Inmirania thermothiophila	strain=DSM 100275	GCA_003751635.1	1750597	1750597	type	True	100.0	867	867	95	conclusive
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	78.6274	405	867	95	below_threshold
Thioalkalivibrio sulfidiphilus	strain=HL-EbGR7	GCA_000021985.1	1033854	1033854	type	True	77.9535	290	867	95	below_threshold
Halorhodospira neutriphila	strain=DSM 15116	GCA_016584055.1	168379	168379	type	True	77.9309	262	867	95	below_threshold
Thiohalobacter thiocyanaticus	strain=Hrh1	GCA_003932505.1	585455	585455	type	True	77.8931	249	867	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_004343155.1	1048	1048	type	True	77.5873	300	867	95	below_threshold
Marichromatium gracile	strain=DSM 203	GCA_016583515.1	1048	1048	type	True	77.5712	298	867	95	below_threshold
Thioalkalivibrio denitrificans	strain=ALJD	GCA_002000365.1	108003	108003	type	True	77.4358	204	867	95	below_threshold
Arhodomonas aquaeolei	strain=DSM 8974	GCA_000374645.1	2369	2369	type	True	77.2733	265	867	95	below_threshold
Halomonas denitrificans	strain=DSM 18045	GCA_003056305.1	370769	370769	type	True	77.2186	276	867	95	below_threshold
Vulcaniibacterium gelatinicum	strain=R-5-52-3	GCA_008033445.1	2598725	2598725	type	True	77.1602	234	867	95	below_threshold
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	77.1389	357	867	95	below_threshold
Allochromatium tepidum	strain=NZ	GCA_018409545.1	553982	553982	type	True	77.1376	196	867	95	below_threshold
Halomonas aestuarii	strain=Hb3	GCA_001886615.1	1897729	1897729	type	True	77.0642	231	867	95	below_threshold
Thioflavicoccus mobilis	strain=8321	GCA_000327045.1	80679	80679	type	True	77.063	218	867	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	76.8891	249	867	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	76.8226	221	867	95	below_threshold
Luteimonas wenzhouensis	strain=YD-1	GCA_007859305.1	2599615	2599615	type	True	76.7929	242	867	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	76.7	228	867	95	below_threshold
Acidihalobacter aeolianus	strain=V6	GCA_001753165.1	2792603	2792603	type	True	76.5188	161	867	95	below_threshold
Dokdonella koreensis	strain=DS-123	GCA_001632775.1	323415	323415	type	True	76.403	222	867	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_002890935.1	2968969	2968969	type	True	76.2321	145	867	95	below_threshold
Rhizobacter gummiphilus	strain=NS21	GCA_002116905.1	946333	946333	type	True	75.7908	234	867	95	below_threshold
Rhizobacter gummiphilus	strain=NBRC 109400	GCA_002762215.1	946333	946333	type	True	75.7788	232	867	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:29:55,821] [INFO] DFAST Taxonomy check result was written to GCF_003751635.1_ASM375163v1_genomic.fna/tc_result.tsv
[2024-01-24 12:29:55,821] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:29:55,822] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:29:55,822] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg365fc2e9-39ab-4e65-89f2-dac23f818a2d/dqc_reference/checkm_data
[2024-01-24 12:29:55,823] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:29:55,857] [INFO] Task started: CheckM
[2024-01-24 12:29:55,857] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003751635.1_ASM375163v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003751635.1_ASM375163v1_genomic.fna/checkm_input GCF_003751635.1_ASM375163v1_genomic.fna/checkm_result
[2024-01-24 12:30:37,628] [INFO] Task succeeded: CheckM
[2024-01-24 12:30:37,630] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:30:37,653] [INFO] ===== Completeness check finished =====
[2024-01-24 12:30:37,653] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:30:37,654] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003751635.1_ASM375163v1_genomic.fna/markers.fasta)
[2024-01-24 12:30:37,654] [INFO] Task started: Blastn
[2024-01-24 12:30:37,654] [INFO] Running command: blastn -query GCF_003751635.1_ASM375163v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg365fc2e9-39ab-4e65-89f2-dac23f818a2d/dqc_reference/reference_markers_gtdb.fasta -out GCF_003751635.1_ASM375163v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:39,527] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:39,531] [INFO] Selected 20 target genomes.
[2024-01-24 12:30:39,531] [INFO] Target genome list was writen to GCF_003751635.1_ASM375163v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:30:39,587] [INFO] Task started: fastANI
[2024-01-24 12:30:39,587] [INFO] Running command: fastANI --query /var/lib/cwl/stg643b560d-955f-4542-a872-5ee72dacfcd9/GCF_003751635.1_ASM375163v1_genomic.fna.gz --refList GCF_003751635.1_ASM375163v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003751635.1_ASM375163v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:30:52,659] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:52,675] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:30:52,675] [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_003751635.1	s__Inmirania thermothiophila	100.0	867	867	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DSM-100275;f__DSM-100275;g__Inmirania	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_015494165.1	s__S144-34 sp015494165	79.8166	353	867	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__S144-34;f__S144-34;g__S144-34	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015487895.1	s__S144-34 sp015487895	79.6524	305	867	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__S144-34;f__S144-34;g__S144-34	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003337735.1	s__Thioalbus denitrificans	78.6276	406	867	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__DSM-26407;f__DSM-26407;g__Thioalbus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015490395.1	s__S141-70 sp015490395	78.5345	206	867	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__S141-70;f__S141-70;g__S141-70	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015491615.1	s__S140-43 sp015491615	78.5038	200	867	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__S140-43;f__S140-43;g__S140-43	95.0	99.42	99.32	0.88	0.87	3	-
GCA_003695825.1	s__J048 sp003695825	78.3066	243	867	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__J048;f__J048;g__J048	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011051715.1	s__HyVt-443 sp011051715	78.0749	289	867	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Sedimenticolaceae;g__HyVt-443	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013348725.1	s__GCA-013348725 sp013348725	77.9835	248	867	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__GCA-013348725;f__GCA-013348725;g__GCA-013348725	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000021985.1	s__Thioalkalivibrio_A sulfidiphilus	77.9695	288	867	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Ectothiorhodospiraceae;g__Thioalkalivibrio_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014762505.1	s__SpSt-1174 sp014762505	77.947	281	867	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__SpSt-1174;f__SpSt-1174;g__SpSt-1174	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002356355.1	s__Thiohalobacter thiocyanaticus_A	77.7713	271	867	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Thiohalobacterales;f__Thiohalobacteraceae;g__Thiohalobacter	95.0	98.53	98.53	0.93	0.93	2	-
GCF_016583835.1	s__Thiococcus pfennigii	77.735	258	867	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Chromatiales;f__Chromatiaceae;g__Thiococcus	95.0	98.97	98.97	0.88	0.88	2	-
GCA_017999615.1	s__JAGNLM01 sp017999615	77.7305	203	867	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__JAABTG01;f__JAABTG01;g__JAGNLM01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000025545.1	s__Thioalkalivibrio sp000025545	77.1155	141	867	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Thioalkalivibrionaceae;g__Thioalkalivibrio	95.0	97.34	97.34	0.93	0.93	2	-
GCF_007859305.1	s__Luteimonas wenzhouensis	76.8117	240	867	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	99.47	99.47	0.98	0.98	2	-
GCA_018241545.1	s__SZAS-83 sp018241545	76.5216	183	867	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__SZAS-83	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016718385.1	s__UBA5518 sp016718385	76.5033	199	867	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__UBA5518;g__UBA5518	95.0	98.99	98.50	0.94	0.92	5	-
GCA_018241525.1	s__SZAS-83 sp018241525	76.2818	275	867	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Steroidobacterales;f__Steroidobacteraceae;g__SZAS-83	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002116905.1	s__Rhizobacter gummiphilus	75.7859	235	867	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhizobacter	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:30:52,678] [INFO] GTDB search result was written to GCF_003751635.1_ASM375163v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:30:52,679] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:30:52,685] [INFO] DFAST_QC result json was written to GCF_003751635.1_ASM375163v1_genomic.fna/dqc_result.json
[2024-01-24 12:30:52,685] [INFO] DFAST_QC completed!
[2024-01-24 12:30:52,685] [INFO] Total running time: 0h1m24s