[2024-01-24 11:43:42,246] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:42,248] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:42,248] [INFO] DQC Reference Directory: /var/lib/cwl/stg0dbfa6d8-b80c-4b60-83ac-971b35d91237/dqc_reference
[2024-01-24 11:43:43,528] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:43,529] [INFO] Task started: Prodigal
[2024-01-24 11:43:43,529] [INFO] Running command: gunzip -c /var/lib/cwl/stg595834d5-fabc-4b87-bfb5-398f1d5a3708/GCF_003073115.1_ASM307311v1_genomic.fna.gz | prodigal -d GCF_003073115.1_ASM307311v1_genomic.fna/cds.fna -a GCF_003073115.1_ASM307311v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:02,070] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:02,071] [INFO] Task started: HMMsearch
[2024-01-24 11:44:02,071] [INFO] Running command: hmmsearch --tblout GCF_003073115.1_ASM307311v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0dbfa6d8-b80c-4b60-83ac-971b35d91237/dqc_reference/reference_markers.hmm GCF_003073115.1_ASM307311v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:02,579] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:02,580] [INFO] Found 6/6 markers.
[2024-01-24 11:44:02,648] [INFO] Query marker FASTA was written to GCF_003073115.1_ASM307311v1_genomic.fna/markers.fasta
[2024-01-24 11:44:02,648] [INFO] Task started: Blastn
[2024-01-24 11:44:02,648] [INFO] Running command: blastn -query GCF_003073115.1_ASM307311v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0dbfa6d8-b80c-4b60-83ac-971b35d91237/dqc_reference/reference_markers.fasta -out GCF_003073115.1_ASM307311v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:03,639] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:03,642] [INFO] Selected 11 target genomes.
[2024-01-24 11:44:03,643] [INFO] Target genome list was writen to GCF_003073115.1_ASM307311v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:03,647] [INFO] Task started: fastANI
[2024-01-24 11:44:03,647] [INFO] Running command: fastANI --query /var/lib/cwl/stg595834d5-fabc-4b87-bfb5-398f1d5a3708/GCF_003073115.1_ASM307311v1_genomic.fna.gz --refList GCF_003073115.1_ASM307311v1_genomic.fna/target_genomes.txt --output GCF_003073115.1_ASM307311v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:17,604] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:17,605] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0dbfa6d8-b80c-4b60-83ac-971b35d91237/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:17,605] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0dbfa6d8-b80c-4b60-83ac-971b35d91237/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:17,615] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:44:17,615] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:17,615] [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 kandeliae	strain=J103	GCA_003073115.1	2073160	2073160	type	True	100.0	2127	2129	95	conclusive
Acuticoccus mangrovi	strain=B2012	GCA_016411865.1	2796142	2796142	type	True	80.6145	960	2129	95	below_threshold
Acuticoccus sediminis	strain=PTG4-2	GCA_003258595.1	2184697	2184697	type	True	79.5927	1033	2129	95	below_threshold
Acuticoccus yangtzensis	strain=JL1095	GCA_003073145.1	1443441	1443441	type	True	79.4099	798	2129	95	below_threshold
Acuticoccus yangtzensis	strain=JL1095	GCA_001927245.1	1443441	1443441	type	True	79.4057	798	2129	95	below_threshold
Rhodobium orientis	strain=DSM 11290	GCA_014197785.1	34017	34017	type	True	77.1388	429	2129	95	below_threshold
Rhodobium orientis	strain=DSM 11290	GCA_003258835.1	34017	34017	type	True	77.0869	422	2129	95	below_threshold
Jiella sonneratiae	strain=MQZ13P-4	GCA_017353515.1	2816856	2816856	type	True	76.957	465	2129	95	below_threshold
Methylobacterium frigidaeris	strain=JCM 32048	GCA_022179185.1	2038277	2038277	type	True	76.3113	526	2129	95	below_threshold
Methylobacterium mesophilicum	strain=NBRC 15688	GCA_022179445.1	39956	39956	type	True	76.2358	339	2129	95	below_threshold
Methylobacterium isbiliense	strain=DSM 17168	GCA_022179325.1	315478	315478	type	True	76.1793	487	2129	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:17,617] [INFO] DFAST Taxonomy check result was written to GCF_003073115.1_ASM307311v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:17,617] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:17,617] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:17,617] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0dbfa6d8-b80c-4b60-83ac-971b35d91237/dqc_reference/checkm_data
[2024-01-24 11:44:17,618] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:17,677] [INFO] Task started: CheckM
[2024-01-24 11:44:17,677] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003073115.1_ASM307311v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003073115.1_ASM307311v1_genomic.fna/checkm_input GCF_003073115.1_ASM307311v1_genomic.fna/checkm_result
[2024-01-24 11:45:45,731] [INFO] Task succeeded: CheckM
[2024-01-24 11:45:45,732] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 24.52%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:45:45,764] [INFO] ===== Completeness check finished =====
[2024-01-24 11:45:45,764] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:45:45,765] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003073115.1_ASM307311v1_genomic.fna/markers.fasta)
[2024-01-24 11:45:45,765] [INFO] Task started: Blastn
[2024-01-24 11:45:45,765] [INFO] Running command: blastn -query GCF_003073115.1_ASM307311v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0dbfa6d8-b80c-4b60-83ac-971b35d91237/dqc_reference/reference_markers_gtdb.fasta -out GCF_003073115.1_ASM307311v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:45:47,386] [INFO] Task succeeded: Blastn
[2024-01-24 11:45:47,390] [INFO] Selected 17 target genomes.
[2024-01-24 11:45:47,391] [INFO] Target genome list was writen to GCF_003073115.1_ASM307311v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:45:47,403] [INFO] Task started: fastANI
[2024-01-24 11:45:47,403] [INFO] Running command: fastANI --query /var/lib/cwl/stg595834d5-fabc-4b87-bfb5-398f1d5a3708/GCF_003073115.1_ASM307311v1_genomic.fna.gz --refList GCF_003073115.1_ASM307311v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003073115.1_ASM307311v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:46:04,252] [INFO] Task succeeded: fastANI
[2024-01-24 11:46:04,270] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:46:04,270] [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	80.6414	957	2129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Amorphaceae;g__Acuticoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003258595.1	s__Acuticoccus sediminis	79.5678	1039	2129	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	79.4297	794	2129	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	77.5455	413	2129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Amorphaceae;g__Amorphus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003258835.1	s__Rhodobium orientis	77.0952	423	2129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Rhodobiaceae;g__Rhodobium	95.0	99.99	99.98	0.99	0.98	3	-
GCF_000192745.1	s__Polymorphum gilvum	77.0716	368	2129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Polymorphum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900185725.1	s__Stappia sp900185725	77.038	479	2129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	98.18	97.99	0.94	0.94	3	-
GCF_900148505.1	s__Pseudoxanthobacter soli	76.865	409	2129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pseudoxanthobacteraceae;g__Pseudoxanthobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009866965.1	s__Propylenella binzhouense	76.8473	423	2129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Afifellaceae;g__Propylenella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017305635.1	s__Bauldia sp017305635	76.7218	426	2129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Kaistiaceae;g__Bauldia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362745.1	s__Oharaeibacter diazotrophicus	76.7085	546	2129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Pleomorphomonadaceae;g__Oharaeibacter	95.0	99.98	99.97	1.00	1.00	3	-
GCF_014635285.1	s__Stappia taiwanensis	76.6404	282	2129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Stappiaceae;g__Stappia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_019160155.1	s__Pinisolibacter aquiterrae	76.4684	468	2129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Ancalomicrobiaceae;g__Pinisolibacter	95.0	96.46	96.46	0.88	0.88	2	-
GCF_011058845.1	s__Methylocystis sp011058845	76.2411	207	2129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylocystis	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000019365.1	s__Methylobacterium sp000019365	76.1392	536	2129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Beijerinckiaceae;g__Methylobacterium	95.0	99.09	99.09	0.89	0.89	2	-
GCF_003116135.1	s__Roseomonas aestuarii	75.7926	347	2129	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009829925.1	s__Roseomonas coralli	75.6568	318	2129	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 11:46:04,271] [INFO] GTDB search result was written to GCF_003073115.1_ASM307311v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:46:04,272] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:46:04,275] [INFO] DFAST_QC result json was written to GCF_003073115.1_ASM307311v1_genomic.fna/dqc_result.json
[2024-01-24 11:46:04,275] [INFO] DFAST_QC completed!
[2024-01-24 11:46:04,276] [INFO] Total running time: 0h2m22s