[2023-06-19 05:51:23,814] [INFO] DFAST_QC pipeline started.
[2023-06-19 05:51:23,817] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 05:51:23,817] [INFO] DQC Reference Directory: /var/lib/cwl/stg3a62a936-1afd-4100-b219-881fb3dbfc28/dqc_reference
[2023-06-19 05:51:25,165] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 05:51:25,166] [INFO] Task started: Prodigal
[2023-06-19 05:51:25,166] [INFO] Running command: gunzip -c /var/lib/cwl/stge9a1490e-bf8e-4101-bdd0-f78d5c9c2e19/GCA_937982005.1_SRR7403881_bin.36_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937982005.1_SRR7403881_bin.36_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937982005.1_SRR7403881_bin.36_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 05:51:31,206] [INFO] Task succeeded: Prodigal
[2023-06-19 05:51:31,207] [INFO] Task started: HMMsearch
[2023-06-19 05:51:31,207] [INFO] Running command: hmmsearch --tblout GCA_937982005.1_SRR7403881_bin.36_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3a62a936-1afd-4100-b219-881fb3dbfc28/dqc_reference/reference_markers.hmm GCA_937982005.1_SRR7403881_bin.36_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-19 05:51:31,451] [INFO] Task succeeded: HMMsearch
[2023-06-19 05:51:31,453] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge9a1490e-bf8e-4101-bdd0-f78d5c9c2e19/GCA_937982005.1_SRR7403881_bin.36_CONCOCT_v1.1_MAG_genomic.fna.gz]
[2023-06-19 05:51:31,484] [INFO] Query marker FASTA was written to GCA_937982005.1_SRR7403881_bin.36_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-19 05:51:31,485] [INFO] Task started: Blastn
[2023-06-19 05:51:31,485] [INFO] Running command: blastn -query GCA_937982005.1_SRR7403881_bin.36_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg3a62a936-1afd-4100-b219-881fb3dbfc28/dqc_reference/reference_markers.fasta -out GCA_937982005.1_SRR7403881_bin.36_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 05:51:32,548] [INFO] Task succeeded: Blastn
[2023-06-19 05:51:32,553] [INFO] Selected 12 target genomes.
[2023-06-19 05:51:32,554] [INFO] Target genome list was writen to GCA_937982005.1_SRR7403881_bin.36_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-19 05:51:32,556] [INFO] Task started: fastANI
[2023-06-19 05:51:32,556] [INFO] Running command: fastANI --query /var/lib/cwl/stge9a1490e-bf8e-4101-bdd0-f78d5c9c2e19/GCA_937982005.1_SRR7403881_bin.36_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937982005.1_SRR7403881_bin.36_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_937982005.1_SRR7403881_bin.36_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 05:51:39,162] [INFO] Task succeeded: fastANI
[2023-06-19 05:51:39,163] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3a62a936-1afd-4100-b219-881fb3dbfc28/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 05:51:39,163] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3a62a936-1afd-4100-b219-881fb3dbfc28/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 05:51:39,180] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 05:51:39,180] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 05:51:39,180] [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
Actinomyces oris	strain=FDAARGOS_1051	GCA_016127955.1	544580	544580	suspected-type	True	94.6083	434	485	95	below_threshold
Actinomyces oris	strain=CCUG 34288	GCA_006546825.1	544580	544580	suspected-type	True	94.5668	435	485	95	below_threshold
Actinomyces naeslundii	strain=NCTC 10301	GCA_001956585.1	1655	1655	type	True	89.1752	422	485	95	below_threshold
Actinomyces naeslundii	strain=Howell 279	GCA_000285995.1	1655	1655	type	True	88.7342	411	485	95	below_threshold
Actinomyces viscosus	strain=NCTC10951	GCA_900637975.1	1656	1656	type	True	88.3441	418	485	95	below_threshold
Actinomyces viscosus	strain=CCUG 14476	GCA_004525795.1	1656	1656	type	True	88.3261	417	485	95	below_threshold
Actinomyces johnsonii	strain=CCUG 34287	GCA_006546835.1	544581	544581	type	True	87.7248	410	485	95	below_threshold
Actinomyces denticolens	strain=DSM 20671	GCA_002072185.1	52767	52767	type	True	81.2444	246	485	95	below_threshold
Actinomyces marmotae	strain=zg-325	GCA_009829655.1	2737173	2737173	type	True	80.7747	236	485	95	below_threshold
Oceanitalea stevensii	strain=Sa1BUA1	GCA_014837105.1	2763072	2763072	type	True	78.1525	135	485	95	below_threshold
Georgenia yuyongxinii	strain=Z443	GCA_006352065.1	2589797	2589797	type	True	77.6305	129	485	95	below_threshold
Ornithinimicrobium kibberense	strain=DSM 17687	GCA_006519705.1	282060	282060	type	True	77.0035	97	485	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 05:51:39,183] [INFO] DFAST Taxonomy check result was written to GCA_937982005.1_SRR7403881_bin.36_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-19 05:51:39,183] [INFO] ===== Taxonomy check completed =====
[2023-06-19 05:51:39,184] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 05:51:39,184] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3a62a936-1afd-4100-b219-881fb3dbfc28/dqc_reference/checkm_data
[2023-06-19 05:51:39,186] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 05:51:39,219] [INFO] Task started: CheckM
[2023-06-19 05:51:39,219] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937982005.1_SRR7403881_bin.36_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937982005.1_SRR7403881_bin.36_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937982005.1_SRR7403881_bin.36_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-19 05:52:02,992] [INFO] Task succeeded: CheckM
[2023-06-19 05:52:02,993] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.29%
Contamintation: 1.04%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 05:52:03,028] [INFO] ===== Completeness check finished =====
[2023-06-19 05:52:03,028] [INFO] ===== Start GTDB Search =====
[2023-06-19 05:52:03,029] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937982005.1_SRR7403881_bin.36_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-19 05:52:03,029] [INFO] Task started: Blastn
[2023-06-19 05:52:03,029] [INFO] Running command: blastn -query GCA_937982005.1_SRR7403881_bin.36_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg3a62a936-1afd-4100-b219-881fb3dbfc28/dqc_reference/reference_markers_gtdb.fasta -out GCA_937982005.1_SRR7403881_bin.36_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 05:52:04,781] [INFO] Task succeeded: Blastn
[2023-06-19 05:52:04,785] [INFO] Selected 6 target genomes.
[2023-06-19 05:52:04,785] [INFO] Target genome list was writen to GCA_937982005.1_SRR7403881_bin.36_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 05:52:04,791] [INFO] Task started: fastANI
[2023-06-19 05:52:04,792] [INFO] Running command: fastANI --query /var/lib/cwl/stge9a1490e-bf8e-4101-bdd0-f78d5c9c2e19/GCA_937982005.1_SRR7403881_bin.36_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937982005.1_SRR7403881_bin.36_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937982005.1_SRR7403881_bin.36_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 05:52:08,398] [INFO] Task succeeded: fastANI
[2023-06-19 05:52:08,410] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 05:52:08,410] [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_001553935.1	s__Actinomyces oris_A	97.283	451	485	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	97.65	97.48	0.94	0.93	4	conclusive
GCF_006546825.1	s__Actinomyces oris	94.5668	435	485	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	96.45	95.25	0.91	0.88	16	-
GCF_001937445.1	s__Actinomyces oris_C	92.8699	443	485	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	97.06	96.78	0.88	0.86	9	-
GCF_001929375.1	s__Actinomyces oris_B	92.0615	425	485	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	98.22	97.84	0.91	0.90	3	-
GCF_001937665.1	s__Actinomyces oris_D	91.5237	425	485	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005696555.1	s__Actinomyces oris_E	91.3745	427	485	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	99.15	98.35	0.98	0.96	3	-
--------------------------------------------------------------------------------
[2023-06-19 05:52:08,415] [INFO] GTDB search result was written to GCA_937982005.1_SRR7403881_bin.36_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-19 05:52:08,416] [INFO] ===== GTDB Search completed =====
[2023-06-19 05:52:08,420] [INFO] DFAST_QC result json was written to GCA_937982005.1_SRR7403881_bin.36_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-19 05:52:08,420] [INFO] DFAST_QC completed!
[2023-06-19 05:52:08,420] [INFO] Total running time: 0h0m45s