[2024-01-24 11:13:04,418] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:13:04,420] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:13:04,420] [INFO] DQC Reference Directory: /var/lib/cwl/stgac5d66e7-b25d-4508-b18d-ba472ed69a7f/dqc_reference
[2024-01-24 11:13:05,663] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:13:05,664] [INFO] Task started: Prodigal
[2024-01-24 11:13:05,664] [INFO] Running command: gunzip -c /var/lib/cwl/stgb6d23176-f4ee-4580-98e3-d7e22a00416e/GCF_016411865.1_ASM1641186v1_genomic.fna.gz | prodigal -d GCF_016411865.1_ASM1641186v1_genomic.fna/cds.fna -a GCF_016411865.1_ASM1641186v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:13:20,960] [INFO] Task succeeded: Prodigal
[2024-01-24 11:13:20,961] [INFO] Task started: HMMsearch
[2024-01-24 11:13:20,961] [INFO] Running command: hmmsearch --tblout GCF_016411865.1_ASM1641186v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgac5d66e7-b25d-4508-b18d-ba472ed69a7f/dqc_reference/reference_markers.hmm GCF_016411865.1_ASM1641186v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:13:21,335] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:13:21,337] [INFO] Found 6/6 markers.
[2024-01-24 11:13:21,388] [INFO] Query marker FASTA was written to GCF_016411865.1_ASM1641186v1_genomic.fna/markers.fasta
[2024-01-24 11:13:21,389] [INFO] Task started: Blastn
[2024-01-24 11:13:21,389] [INFO] Running command: blastn -query GCF_016411865.1_ASM1641186v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgac5d66e7-b25d-4508-b18d-ba472ed69a7f/dqc_reference/reference_markers.fasta -out GCF_016411865.1_ASM1641186v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:22,394] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:22,398] [INFO] Selected 15 target genomes.
[2024-01-24 11:13:22,399] [INFO] Target genome list was writen to GCF_016411865.1_ASM1641186v1_genomic.fna/target_genomes.txt
[2024-01-24 11:13:22,406] [INFO] Task started: fastANI
[2024-01-24 11:13:22,406] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6d23176-f4ee-4580-98e3-d7e22a00416e/GCF_016411865.1_ASM1641186v1_genomic.fna.gz --refList GCF_016411865.1_ASM1641186v1_genomic.fna/target_genomes.txt --output GCF_016411865.1_ASM1641186v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:40,577] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:40,577] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgac5d66e7-b25d-4508-b18d-ba472ed69a7f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:40,578] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgac5d66e7-b25d-4508-b18d-ba472ed69a7f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:40,601] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:13:40,602] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:13:40,602] [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
Acuticoccus mangrovi	strain=B2012	GCA_016411865.1	2796142	2796142	type	True	100.0	1785	1790	95	conclusive
Acuticoccus kandeliae	strain=J103	GCA_003073115.1	2073160	2073160	type	True	80.6203	955	1790	95	below_threshold
Acuticoccus sediminis	strain=PTG4-2	GCA_003258595.1	2184697	2184697	type	True	79.6446	904	1790	95	below_threshold
Acuticoccus yangtzensis	strain=JL1095	GCA_003073145.1	1443441	1443441	type	True	79.3583	762	1790	95	below_threshold
Acuticoccus yangtzensis	strain=JL1095	GCA_001927245.1	1443441	1443441	type	True	79.3347	759	1790	95	below_threshold
Chelatococcus caeni	strain=DSM 103737	GCA_014196925.1	1348468	1348468	type	True	76.9838	470	1790	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	76.9825	451	1790	95	below_threshold
Methylobacterium terrae	strain=17Sr1-28	GCA_003173755.1	2202827	2202827	type	True	76.6101	492	1790	95	below_threshold
Methylobacterium oxalidis	strain=DSM 24028	GCA_022179505.1	944322	944322	type	True	76.5142	376	1790	95	below_threshold
Methylobacterium oryzihabitans	strain=TER-1	GCA_004004555.2	2499852	2499852	type	True	76.5076	491	1790	95	below_threshold
Methylobacterium oxalidis	strain=NBRC 107715	GCA_007992195.1	944322	944322	type	True	76.4883	377	1790	95	below_threshold
Methylobacterium terricola	strain=17Sr1-39	GCA_006151805.1	2583531	2583531	type	True	76.4626	504	1790	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	76.3626	530	1790	95	below_threshold
Amaricoccus solimangrovi	strain=HB172011	GCA_006385685.1	2589815	2589815	type	True	76.2361	349	1790	95	below_threshold
Roseomonas rhizosphaerae	strain=YW11	GCA_002631185.1	1335062	1335062	type	True	75.9882	319	1790	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:40,604] [INFO] DFAST Taxonomy check result was written to GCF_016411865.1_ASM1641186v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:40,604] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:40,604] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:40,605] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgac5d66e7-b25d-4508-b18d-ba472ed69a7f/dqc_reference/checkm_data
[2024-01-24 11:13:40,606] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:40,660] [INFO] Task started: CheckM
[2024-01-24 11:13:40,660] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016411865.1_ASM1641186v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016411865.1_ASM1641186v1_genomic.fna/checkm_input GCF_016411865.1_ASM1641186v1_genomic.fna/checkm_result
[2024-01-24 11:14:30,501] [INFO] Task succeeded: CheckM
[2024-01-24 11:14:30,502] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:14:30,523] [INFO] ===== Completeness check finished =====
[2024-01-24 11:14:30,524] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:14:30,524] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016411865.1_ASM1641186v1_genomic.fna/markers.fasta)
[2024-01-24 11:14:30,524] [INFO] Task started: Blastn
[2024-01-24 11:14:30,525] [INFO] Running command: blastn -query GCF_016411865.1_ASM1641186v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgac5d66e7-b25d-4508-b18d-ba472ed69a7f/dqc_reference/reference_markers_gtdb.fasta -out GCF_016411865.1_ASM1641186v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:14:32,527] [INFO] Task succeeded: Blastn
[2024-01-24 11:14:32,531] [INFO] Selected 21 target genomes.
[2024-01-24 11:14:32,532] [INFO] Target genome list was writen to GCF_016411865.1_ASM1641186v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:14:32,551] [INFO] Task started: fastANI
[2024-01-24 11:14:32,551] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6d23176-f4ee-4580-98e3-d7e22a00416e/GCF_016411865.1_ASM1641186v1_genomic.fna.gz --refList GCF_016411865.1_ASM1641186v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016411865.1_ASM1641186v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:14:52,076] [INFO] Task succeeded: fastANI
[2024-01-24 11:14:52,099] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:14:52,100] [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_016411865.1	s__Acuticoccus sp016411865	100.0	1785	1790	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Amorphaceae;g__Acuticoccus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003258595.1	s__Acuticoccus sediminis	79.6556	901	1790	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Amorphaceae;g__Acuticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001927245.1	s__Acuticoccus yangtzensis	79.3749	754	1790	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Amorphaceae;g__Acuticoccus	95.0	98.76	97.53	0.97	0.95	3	-
GCF_000374525.1	s__Amorphus coralli	77.6742	425	1790	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Amorphaceae;g__Amorphus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900185725.1	s__Stappia sp900185725	77.3925	428	1790	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	98.18	97.99	0.94	0.94	3	-
GCF_015904235.1	s__L22 sp015904235	77.2387	514	1790	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__L22	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003258835.1	s__Rhodobium orientis	77.0461	417	1790	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhodobiaceae;g__Rhodobium	95.0	99.99	99.98	0.99	0.98	3	-
GCA_002722295.1	s__Stappia sp002722295	77.0063	308	1790	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	99.88	99.88	0.88	0.88	2	-
GCF_007559435.1	s__Starkeya sp007559435	76.9978	374	1790	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Starkeya	95.0	98.55	98.55	0.95	0.95	2	-
GCF_014196925.1	s__Chelatococcus_A caeni	76.9561	476	1790	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Chelatococcus_A	95.0	98.75	98.72	0.96	0.95	3	-
GCF_001418005.1	s__Chelatococcus_A sambhunathii	76.9155	362	1790	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Chelatococcus_A	95.0	99.33	99.03	0.97	0.94	5	-
GCA_017305635.1	s__Bauldia sp017305635	76.8811	356	1790	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Bauldia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017305835.1	s__RCIO01 sp017305835	76.8755	448	1790	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhizobiaceae;g__RCIO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002298965.1	s__Pinisolibacter sp002298965	76.7399	361	1790	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Ancalomicrobiaceae;g__Pinisolibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003173755.1	s__Methylobacterium terrae	76.5662	500	1790	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007992195.1	s__Methylobacterium oxalidis	76.4816	376	1790	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002778835.1	s__Methylobacterium sp002778835	76.4478	342	1790	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	99.93	99.92	0.96	0.96	4	-
GCF_001653715.1	s__Methylobacterium platani	76.3871	537	1790	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	99.94	99.94	0.97	0.97	2	-
GCA_002721365.1	s__GCA-2721365 sp002721365	76.0808	175	1790	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__GCA-2721365;f__GCA-2721365;g__GCA-2721365	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002631185.1	s__Roseomonas rhizosphaerae	75.9807	319	1790	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003116135.1	s__Roseomonas aestuarii	75.8865	333	1790	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:14:52,101] [INFO] GTDB search result was written to GCF_016411865.1_ASM1641186v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:14:52,102] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:14:52,106] [INFO] DFAST_QC result json was written to GCF_016411865.1_ASM1641186v1_genomic.fna/dqc_result.json
[2024-01-24 11:14:52,106] [INFO] DFAST_QC completed!
[2024-01-24 11:14:52,106] [INFO] Total running time: 0h1m48s