[2023-06-29 19:44:46,957] [INFO] DFAST_QC pipeline started.
[2023-06-29 19:44:46,959] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 19:44:46,959] [INFO] DQC Reference Directory: /var/lib/cwl/stg542514d7-016a-4a0c-9b52-7bf92dcbd442/dqc_reference
[2023-06-29 19:44:50,105] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 19:44:50,106] [INFO] Task started: Prodigal
[2023-06-29 19:44:50,106] [INFO] Running command: gunzip -c /var/lib/cwl/stg11306ae6-ac92-45d5-8c8b-d799fc25b668/GCA_937874285.1_SRR1561991_bin.137_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937874285.1_SRR1561991_bin.137_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937874285.1_SRR1561991_bin.137_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 19:44:55,185] [INFO] Task succeeded: Prodigal
[2023-06-29 19:44:55,185] [INFO] Task started: HMMsearch
[2023-06-29 19:44:55,186] [INFO] Running command: hmmsearch --tblout GCA_937874285.1_SRR1561991_bin.137_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg542514d7-016a-4a0c-9b52-7bf92dcbd442/dqc_reference/reference_markers.hmm GCA_937874285.1_SRR1561991_bin.137_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-29 19:44:55,399] [INFO] Task succeeded: HMMsearch
[2023-06-29 19:44:55,400] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg11306ae6-ac92-45d5-8c8b-d799fc25b668/GCA_937874285.1_SRR1561991_bin.137_CONCOCT_v1.1_MAG_genomic.fna.gz]
[2023-06-29 19:44:55,429] [INFO] Query marker FASTA was written to GCA_937874285.1_SRR1561991_bin.137_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-29 19:44:55,430] [INFO] Task started: Blastn
[2023-06-29 19:44:55,430] [INFO] Running command: blastn -query GCA_937874285.1_SRR1561991_bin.137_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg542514d7-016a-4a0c-9b52-7bf92dcbd442/dqc_reference/reference_markers.fasta -out GCA_937874285.1_SRR1561991_bin.137_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 19:44:56,057] [INFO] Task succeeded: Blastn
[2023-06-29 19:44:56,063] [INFO] Selected 12 target genomes.
[2023-06-29 19:44:56,064] [INFO] Target genome list was writen to GCA_937874285.1_SRR1561991_bin.137_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-29 19:44:56,066] [INFO] Task started: fastANI
[2023-06-29 19:44:56,066] [INFO] Running command: fastANI --query /var/lib/cwl/stg11306ae6-ac92-45d5-8c8b-d799fc25b668/GCA_937874285.1_SRR1561991_bin.137_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937874285.1_SRR1561991_bin.137_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_937874285.1_SRR1561991_bin.137_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 19:45:02,924] [INFO] Task succeeded: fastANI
[2023-06-29 19:45:02,924] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg542514d7-016a-4a0c-9b52-7bf92dcbd442/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 19:45:02,925] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg542514d7-016a-4a0c-9b52-7bf92dcbd442/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 19:45:02,940] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2023-06-29 19:45:02,940] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2023-06-29 19:45:02,940] [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
Sinirhodobacter huangdaonensis	strain=CGMCC 1.12963	GCA_004022465.1	2501515	2501515	type	True	95.9504	159	164	95	inconclusive
Sinirhodobacter ferrireducens	strain=CCTCC AB2012026	GCA_004022265.1	1215032	1215032	type	True	95.4013	159	164	95	inconclusive
Sinirhodobacter hankyongi	strain=BO-81	GCA_003664585.1	2294033	2294033	type	True	94.164	147	164	95	below_threshold
Rhodobacter capsulatus	strain=DSM 1710	GCA_003254295.1	1061	1061	type	True	81.9988	109	164	95	below_threshold
Rhodobacter viridis	strain=JA737	GCA_003217355.1	1054202	1054202	type	True	81.7994	113	164	95	below_threshold
Thioclava atlantica	strain=13D2W-2	GCA_000737065.1	1317124	1317124	type	True	81.0038	108	164	95	below_threshold
Thioclava pacifica	strain=DSM 10166	GCA_000714535.1	285109	285109	type	True	80.2886	96	164	95	below_threshold
Paracoccus mutanolyticus	strain=RSP-02	GCA_003285265.1	1499308	1499308	type	True	79.561	77	164	95	below_threshold
Cereibacter ovatus	strain=JA234	GCA_900207575.1	439529	439529	type	True	79.2103	78	164	95	below_threshold
Paracoccus shandongensis	strain=wg2	GCA_017315735.1	2816048	2816048	type	True	78.4108	74	164	95	below_threshold
Pseudogemmobacter bohemicus	strain=Cd-10	GCA_003290025.1	2250708	2250708	type	True	77.7461	67	164	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 19:45:02,943] [INFO] DFAST Taxonomy check result was written to GCA_937874285.1_SRR1561991_bin.137_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-29 19:45:02,943] [INFO] ===== Taxonomy check completed =====
[2023-06-29 19:45:02,943] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 19:45:02,943] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg542514d7-016a-4a0c-9b52-7bf92dcbd442/dqc_reference/checkm_data
[2023-06-29 19:45:02,944] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 19:45:02,980] [INFO] Task started: CheckM
[2023-06-29 19:45:02,981] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937874285.1_SRR1561991_bin.137_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937874285.1_SRR1561991_bin.137_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937874285.1_SRR1561991_bin.137_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-29 19:45:24,994] [INFO] Task succeeded: CheckM
[2023-06-29 19:45:24,995] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.80%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 19:45:25,021] [INFO] ===== Completeness check finished =====
[2023-06-29 19:45:25,021] [INFO] ===== Start GTDB Search =====
[2023-06-29 19:45:25,022] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937874285.1_SRR1561991_bin.137_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-29 19:45:25,023] [INFO] Task started: Blastn
[2023-06-29 19:45:25,023] [INFO] Running command: blastn -query GCA_937874285.1_SRR1561991_bin.137_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg542514d7-016a-4a0c-9b52-7bf92dcbd442/dqc_reference/reference_markers_gtdb.fasta -out GCA_937874285.1_SRR1561991_bin.137_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 19:45:25,845] [INFO] Task succeeded: Blastn
[2023-06-29 19:45:25,850] [INFO] Selected 9 target genomes.
[2023-06-29 19:45:25,850] [INFO] Target genome list was writen to GCA_937874285.1_SRR1561991_bin.137_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 19:45:25,855] [INFO] Task started: fastANI
[2023-06-29 19:45:25,855] [INFO] Running command: fastANI --query /var/lib/cwl/stg11306ae6-ac92-45d5-8c8b-d799fc25b668/GCA_937874285.1_SRR1561991_bin.137_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937874285.1_SRR1561991_bin.137_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937874285.1_SRR1561991_bin.137_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 19:45:31,055] [INFO] Task succeeded: fastANI
[2023-06-29 19:45:31,070] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 19:45:31,071] [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_004022265.1	s__Paenirhodobacter ferrireducens	95.4013	159	164	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paenirhodobacter	95.0	96.45	95.14	0.91	0.87	4	conclusive
GCF_003664585.1	s__Paenirhodobacter hankyongi	94.164	147	164	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paenirhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001856665.1	s__LPB0142 sp001856665	82.7405	118	164	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__LPB0142	95.0	98.52	98.52	0.91	0.91	2	-
GCA_003249215.1	s__SZUA-611 sp003249215	82.6185	95	164	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__SZUA-611	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000740785.1	s__Paenirhodobacter enshiensis	82.0707	111	164	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paenirhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003254295.1	s__Rhodobacter capsulatus	81.9988	109	164	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter	95.0	99.61	98.47	0.97	0.92	5	-
GCF_005144475.1	s__Rhodobacter capsulatus_C	81.9513	112	164	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003217355.1	s__Rhodobacter viridis	81.7994	113	164	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Rhodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004022215.1	s__Paenirhodobacter populi	81.2449	113	164	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paenirhodobacter	95.0	97.06	96.55	0.86	0.79	5	-
--------------------------------------------------------------------------------
[2023-06-29 19:45:31,073] [INFO] GTDB search result was written to GCA_937874285.1_SRR1561991_bin.137_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-29 19:45:31,074] [INFO] ===== GTDB Search completed =====
[2023-06-29 19:45:31,078] [INFO] DFAST_QC result json was written to GCA_937874285.1_SRR1561991_bin.137_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-29 19:45:31,078] [INFO] DFAST_QC completed!
[2023-06-29 19:45:31,078] [INFO] Total running time: 0h0m44s