[2023-06-05 12:00:10,477] [INFO] DFAST_QC pipeline started.
[2023-06-05 12:00:10,479] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 12:00:10,480] [INFO] DQC Reference Directory: /var/lib/cwl/stg979ba76b-7546-4cea-b135-95a16745a66b/dqc_reference
[2023-06-05 12:00:12,719] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 12:00:12,720] [INFO] Task started: Prodigal
[2023-06-05 12:00:12,720] [INFO] Running command: gunzip -c /var/lib/cwl/stg09c4162f-4bc7-46c7-9b89-0b158b048cca/GCA_934718065.1_ERR7738582_bin.115_genomic.fna.gz | prodigal -d GCA_934718065.1_ERR7738582_bin.115_genomic.fna/cds.fna -a GCA_934718065.1_ERR7738582_bin.115_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 12:00:17,611] [INFO] Task succeeded: Prodigal
[2023-06-05 12:00:17,611] [INFO] Task started: HMMsearch
[2023-06-05 12:00:17,611] [INFO] Running command: hmmsearch --tblout GCA_934718065.1_ERR7738582_bin.115_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg979ba76b-7546-4cea-b135-95a16745a66b/dqc_reference/reference_markers.hmm GCA_934718065.1_ERR7738582_bin.115_genomic.fna/protein.faa > /dev/null
[2023-06-05 12:00:17,863] [INFO] Task succeeded: HMMsearch
[2023-06-05 12:00:17,864] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg09c4162f-4bc7-46c7-9b89-0b158b048cca/GCA_934718065.1_ERR7738582_bin.115_genomic.fna.gz]
[2023-06-05 12:00:17,890] [INFO] Query marker FASTA was written to GCA_934718065.1_ERR7738582_bin.115_genomic.fna/markers.fasta
[2023-06-05 12:00:17,890] [INFO] Task started: Blastn
[2023-06-05 12:00:17,890] [INFO] Running command: blastn -query GCA_934718065.1_ERR7738582_bin.115_genomic.fna/markers.fasta -db /var/lib/cwl/stg979ba76b-7546-4cea-b135-95a16745a66b/dqc_reference/reference_markers.fasta -out GCA_934718065.1_ERR7738582_bin.115_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 12:00:18,484] [INFO] Task succeeded: Blastn
[2023-06-05 12:00:18,489] [INFO] Selected 13 target genomes.
[2023-06-05 12:00:18,490] [INFO] Target genome list was writen to GCA_934718065.1_ERR7738582_bin.115_genomic.fna/target_genomes.txt
[2023-06-05 12:00:18,494] [INFO] Task started: fastANI
[2023-06-05 12:00:18,495] [INFO] Running command: fastANI --query /var/lib/cwl/stg09c4162f-4bc7-46c7-9b89-0b158b048cca/GCA_934718065.1_ERR7738582_bin.115_genomic.fna.gz --refList GCA_934718065.1_ERR7738582_bin.115_genomic.fna/target_genomes.txt --output GCA_934718065.1_ERR7738582_bin.115_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 12:00:25,464] [INFO] Task succeeded: fastANI
[2023-06-05 12:00:25,465] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg979ba76b-7546-4cea-b135-95a16745a66b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 12:00:25,465] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg979ba76b-7546-4cea-b135-95a16745a66b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 12:00:25,477] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 12:00:25,477] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 12:00:25,478] [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
Treponema porcinum	strain=ATCC BAA-908	GCA_900167145.1	261392	261392	type	True	77.7369	133	689	95	below_threshold
Treponema succinifaciens	strain=DSM 2489	GCA_000195275.1	167	167	type	True	77.5518	92	689	95	below_threshold
Treponema berlinense	strain=ATCC BAA-909	GCA_900167025.1	225004	225004	type	True	77.2548	81	689	95	below_threshold
Treponema rectale	strain=DSM 103679	GCA_014202035.1	744512	744512	suspected-type	True	76.5929	52	689	95	below_threshold
Treponema ruminis	strain=DSM 103462	GCA_014201975.1	744515	744515	type	True	76.202	60	689	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 12:00:25,480] [INFO] DFAST Taxonomy check result was written to GCA_934718065.1_ERR7738582_bin.115_genomic.fna/tc_result.tsv
[2023-06-05 12:00:25,481] [INFO] ===== Taxonomy check completed =====
[2023-06-05 12:00:25,481] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 12:00:25,482] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg979ba76b-7546-4cea-b135-95a16745a66b/dqc_reference/checkm_data
[2023-06-05 12:00:25,484] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 12:00:25,515] [INFO] Task started: CheckM
[2023-06-05 12:00:25,515] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934718065.1_ERR7738582_bin.115_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934718065.1_ERR7738582_bin.115_genomic.fna/checkm_input GCA_934718065.1_ERR7738582_bin.115_genomic.fna/checkm_result
[2023-06-05 12:00:47,545] [INFO] Task succeeded: CheckM
[2023-06-05 12:00:47,547] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 12:00:47,577] [INFO] ===== Completeness check finished =====
[2023-06-05 12:00:47,577] [INFO] ===== Start GTDB Search =====
[2023-06-05 12:00:47,578] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934718065.1_ERR7738582_bin.115_genomic.fna/markers.fasta)
[2023-06-05 12:00:47,578] [INFO] Task started: Blastn
[2023-06-05 12:00:47,578] [INFO] Running command: blastn -query GCA_934718065.1_ERR7738582_bin.115_genomic.fna/markers.fasta -db /var/lib/cwl/stg979ba76b-7546-4cea-b135-95a16745a66b/dqc_reference/reference_markers_gtdb.fasta -out GCA_934718065.1_ERR7738582_bin.115_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 12:00:48,555] [INFO] Task succeeded: Blastn
[2023-06-05 12:00:48,560] [INFO] Selected 13 target genomes.
[2023-06-05 12:00:48,560] [INFO] Target genome list was writen to GCA_934718065.1_ERR7738582_bin.115_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 12:00:48,569] [INFO] Task started: fastANI
[2023-06-05 12:00:48,569] [INFO] Running command: fastANI --query /var/lib/cwl/stg09c4162f-4bc7-46c7-9b89-0b158b048cca/GCA_934718065.1_ERR7738582_bin.115_genomic.fna.gz --refList GCA_934718065.1_ERR7738582_bin.115_genomic.fna/target_genomes_gtdb.txt --output GCA_934718065.1_ERR7738582_bin.115_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 12:00:54,818] [INFO] Task succeeded: fastANI
[2023-06-05 12:00:54,839] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-05 12:00:54,840] [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_002478955.1	s__Treponema_D sp002478955	83.3595	463	689	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	97.79	97.79	0.82	0.82	2	-
GCA_900317625.1	s__Treponema_D sp900317625	83.2376	455	689	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	99.21	99.03	0.90	0.87	4	-
GCA_900541945.1	s__Treponema_D sp900541945	82.5746	463	689	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	97.94	97.90	0.88	0.87	3	-
GCA_017381365.1	s__Treponema_D sp017381365	77.7504	146	689	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	97.14	97.14	0.75	0.75	2	-
GCF_900167145.1	s__Treponema_D porcinum	77.7369	133	689	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	97.53	96.24	0.92	0.88	5	-
GCA_017392945.1	s__Treponema_D sp017392945	77.528	122	689	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017386165.1	s__Treponema_D sp017386165	77.3902	81	689	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002449305.1	s__Treponema_D sp002449305	77.2009	107	689	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	98.77	97.10	0.90	0.86	10	-
GCA_902797305.1	s__Treponema_D sp902797305	77.129	64	689	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017390125.1	s__Treponema_D sp017390125	77.0205	87	689	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016117655.1	s__Treponema_D sp900541995	76.6397	55	689	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	98.86	98.78	0.96	0.96	3	-
GCF_014334335.1	s__Treponema_D sp014334335	76.3229	57	689	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Treponematales;f__Treponemataceae;g__Treponema_D	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 12:00:54,843] [INFO] GTDB search result was written to GCA_934718065.1_ERR7738582_bin.115_genomic.fna/result_gtdb.tsv
[2023-06-05 12:00:54,843] [INFO] ===== GTDB Search completed =====
[2023-06-05 12:00:54,847] [INFO] DFAST_QC result json was written to GCA_934718065.1_ERR7738582_bin.115_genomic.fna/dqc_result.json
[2023-06-05 12:00:54,848] [INFO] DFAST_QC completed!
[2023-06-05 12:00:54,848] [INFO] Total running time: 0h0m44s