[2023-06-30 03:33:16,965] [INFO] DFAST_QC pipeline started.
[2023-06-30 03:33:16,967] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 03:33:16,968] [INFO] DQC Reference Directory: /var/lib/cwl/stgcf1f5b2b-78c1-4779-bfae-b39b18afcb30/dqc_reference
[2023-06-30 03:33:18,226] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 03:33:18,227] [INFO] Task started: Prodigal
[2023-06-30 03:33:18,228] [INFO] Running command: gunzip -c /var/lib/cwl/stgdb7df5a4-a546-468e-919c-ef0ee5ef7008/GCA_903874265.1_freshwater_MAG_---_Day6-6_bin-363_genomic.fna.gz | prodigal -d GCA_903874265.1_freshwater_MAG_---_Day6-6_bin-363_genomic.fna/cds.fna -a GCA_903874265.1_freshwater_MAG_---_Day6-6_bin-363_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 03:33:24,731] [INFO] Task succeeded: Prodigal
[2023-06-30 03:33:24,732] [INFO] Task started: HMMsearch
[2023-06-30 03:33:24,732] [INFO] Running command: hmmsearch --tblout GCA_903874265.1_freshwater_MAG_---_Day6-6_bin-363_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcf1f5b2b-78c1-4779-bfae-b39b18afcb30/dqc_reference/reference_markers.hmm GCA_903874265.1_freshwater_MAG_---_Day6-6_bin-363_genomic.fna/protein.faa > /dev/null
[2023-06-30 03:33:24,973] [INFO] Task succeeded: HMMsearch
[2023-06-30 03:33:24,975] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgdb7df5a4-a546-468e-919c-ef0ee5ef7008/GCA_903874265.1_freshwater_MAG_---_Day6-6_bin-363_genomic.fna.gz]
[2023-06-30 03:33:25,002] [INFO] Query marker FASTA was written to GCA_903874265.1_freshwater_MAG_---_Day6-6_bin-363_genomic.fna/markers.fasta
[2023-06-30 03:33:25,002] [INFO] Task started: Blastn
[2023-06-30 03:33:25,002] [INFO] Running command: blastn -query GCA_903874265.1_freshwater_MAG_---_Day6-6_bin-363_genomic.fna/markers.fasta -db /var/lib/cwl/stgcf1f5b2b-78c1-4779-bfae-b39b18afcb30/dqc_reference/reference_markers.fasta -out GCA_903874265.1_freshwater_MAG_---_Day6-6_bin-363_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 03:33:25,568] [INFO] Task succeeded: Blastn
[2023-06-30 03:33:25,573] [INFO] Selected 10 target genomes.
[2023-06-30 03:33:25,574] [INFO] Target genome list was writen to GCA_903874265.1_freshwater_MAG_---_Day6-6_bin-363_genomic.fna/target_genomes.txt
[2023-06-30 03:33:25,576] [INFO] Task started: fastANI
[2023-06-30 03:33:25,576] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb7df5a4-a546-468e-919c-ef0ee5ef7008/GCA_903874265.1_freshwater_MAG_---_Day6-6_bin-363_genomic.fna.gz --refList GCA_903874265.1_freshwater_MAG_---_Day6-6_bin-363_genomic.fna/target_genomes.txt --output GCA_903874265.1_freshwater_MAG_---_Day6-6_bin-363_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 03:33:30,784] [INFO] Task succeeded: fastANI
[2023-06-30 03:33:30,785] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcf1f5b2b-78c1-4779-bfae-b39b18afcb30/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 03:33:30,785] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcf1f5b2b-78c1-4779-bfae-b39b18afcb30/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 03:33:30,793] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 03:33:30,793] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 03:33:30,794] [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
Pelodictyon phaeoclathratiforme	strain=BU-1	GCA_000020645.1	34090	34090	type	True	79.426	331	694	95	below_threshold
Chlorobium ferrooxidans	strain=DSM 13031	GCA_000168715.1	84205	84205	type	True	77.7615	205	694	95	below_threshold
Chlorobium limicola	strain=DSM 245	GCA_000020465.1	1092	1092	type	True	76.6177	89	694	95	below_threshold
Chlorobium phaeobacteroides	strain=DSM 266	GCA_000015125.1	1096	1096	type	True	76.5524	109	694	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 03:33:30,796] [INFO] DFAST Taxonomy check result was written to GCA_903874265.1_freshwater_MAG_---_Day6-6_bin-363_genomic.fna/tc_result.tsv
[2023-06-30 03:33:30,796] [INFO] ===== Taxonomy check completed =====
[2023-06-30 03:33:30,796] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 03:33:30,797] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcf1f5b2b-78c1-4779-bfae-b39b18afcb30/dqc_reference/checkm_data
[2023-06-30 03:33:30,798] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 03:33:30,829] [INFO] Task started: CheckM
[2023-06-30 03:33:30,830] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903874265.1_freshwater_MAG_---_Day6-6_bin-363_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903874265.1_freshwater_MAG_---_Day6-6_bin-363_genomic.fna/checkm_input GCA_903874265.1_freshwater_MAG_---_Day6-6_bin-363_genomic.fna/checkm_result
[2023-06-30 03:34:08,515] [INFO] Task succeeded: CheckM
[2023-06-30 03:34:08,517] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 88.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 03:34:08,538] [INFO] ===== Completeness check finished =====
[2023-06-30 03:34:08,538] [INFO] ===== Start GTDB Search =====
[2023-06-30 03:34:08,538] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903874265.1_freshwater_MAG_---_Day6-6_bin-363_genomic.fna/markers.fasta)
[2023-06-30 03:34:08,539] [INFO] Task started: Blastn
[2023-06-30 03:34:08,539] [INFO] Running command: blastn -query GCA_903874265.1_freshwater_MAG_---_Day6-6_bin-363_genomic.fna/markers.fasta -db /var/lib/cwl/stgcf1f5b2b-78c1-4779-bfae-b39b18afcb30/dqc_reference/reference_markers_gtdb.fasta -out GCA_903874265.1_freshwater_MAG_---_Day6-6_bin-363_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 03:34:09,324] [INFO] Task succeeded: Blastn
[2023-06-30 03:34:09,329] [INFO] Selected 7 target genomes.
[2023-06-30 03:34:09,329] [INFO] Target genome list was writen to GCA_903874265.1_freshwater_MAG_---_Day6-6_bin-363_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 03:34:09,334] [INFO] Task started: fastANI
[2023-06-30 03:34:09,334] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb7df5a4-a546-468e-919c-ef0ee5ef7008/GCA_903874265.1_freshwater_MAG_---_Day6-6_bin-363_genomic.fna.gz --refList GCA_903874265.1_freshwater_MAG_---_Day6-6_bin-363_genomic.fna/target_genomes_gtdb.txt --output GCA_903874265.1_freshwater_MAG_---_Day6-6_bin-363_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 03:34:13,282] [INFO] Task succeeded: fastANI
[2023-06-30 03:34:13,293] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 03:34:13,294] [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_903994455.1	s__Chlorobium sp903994455	99.7163	599	694	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.65	99.40	0.86	0.85	13	conclusive
GCA_903937835.1	s__Chlorobium sp903937835	87.9517	498	694	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.77	99.60	0.93	0.86	6	-
GCA_903836465.1	s__Chlorobium sp903836465	87.5919	489	694	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.30	97.63	0.95	0.90	12	-
GCA_903887845.1	s__Chlorobium sp903887845	87.4677	475	694	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.96	99.96	0.95	0.95	2	-
GCA_903929845.1	s__Chlorobium sp903929845	86.6745	348	694	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.53	99.40	0.83	0.81	5	-
GCA_903843305.1	s__Chlorobium sp903843305	82.9431	426	694	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	98.98	96.88	0.93	0.82	17	-
GCA_903865705.1	s__Chlorobium sp903865705	79.2024	272	694	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.47	99.06	0.91	0.87	5	-
--------------------------------------------------------------------------------
[2023-06-30 03:34:13,296] [INFO] GTDB search result was written to GCA_903874265.1_freshwater_MAG_---_Day6-6_bin-363_genomic.fna/result_gtdb.tsv
[2023-06-30 03:34:13,296] [INFO] ===== GTDB Search completed =====
[2023-06-30 03:34:13,300] [INFO] DFAST_QC result json was written to GCA_903874265.1_freshwater_MAG_---_Day6-6_bin-363_genomic.fna/dqc_result.json
[2023-06-30 03:34:13,300] [INFO] DFAST_QC completed!
[2023-06-30 03:34:13,300] [INFO] Total running time: 0h0m56s