[2023-06-29 22:29:44,862] [INFO] DFAST_QC pipeline started.
[2023-06-29 22:29:44,866] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 22:29:44,867] [INFO] DQC Reference Directory: /var/lib/cwl/stg1aeddec5-4642-4b47-84ae-9e48f6e42890/dqc_reference
[2023-06-29 22:29:46,082] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 22:29:46,083] [INFO] Task started: Prodigal
[2023-06-29 22:29:46,083] [INFO] Running command: gunzip -c /var/lib/cwl/stga28f12d1-55e7-4ff3-80f5-da7835e1a6c4/GCA_903916475.1_freshwater_MAG_---_LJ-5-9m_bin-0497_genomic.fna.gz | prodigal -d GCA_903916475.1_freshwater_MAG_---_LJ-5-9m_bin-0497_genomic.fna/cds.fna -a GCA_903916475.1_freshwater_MAG_---_LJ-5-9m_bin-0497_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 22:29:51,028] [INFO] Task succeeded: Prodigal
[2023-06-29 22:29:51,028] [INFO] Task started: HMMsearch
[2023-06-29 22:29:51,028] [INFO] Running command: hmmsearch --tblout GCA_903916475.1_freshwater_MAG_---_LJ-5-9m_bin-0497_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1aeddec5-4642-4b47-84ae-9e48f6e42890/dqc_reference/reference_markers.hmm GCA_903916475.1_freshwater_MAG_---_LJ-5-9m_bin-0497_genomic.fna/protein.faa > /dev/null
[2023-06-29 22:29:51,262] [INFO] Task succeeded: HMMsearch
[2023-06-29 22:29:51,264] [WARNING] Found 5/6 markers. [/var/lib/cwl/stga28f12d1-55e7-4ff3-80f5-da7835e1a6c4/GCA_903916475.1_freshwater_MAG_---_LJ-5-9m_bin-0497_genomic.fna.gz]
[2023-06-29 22:29:51,291] [INFO] Query marker FASTA was written to GCA_903916475.1_freshwater_MAG_---_LJ-5-9m_bin-0497_genomic.fna/markers.fasta
[2023-06-29 22:29:51,291] [INFO] Task started: Blastn
[2023-06-29 22:29:51,291] [INFO] Running command: blastn -query GCA_903916475.1_freshwater_MAG_---_LJ-5-9m_bin-0497_genomic.fna/markers.fasta -db /var/lib/cwl/stg1aeddec5-4642-4b47-84ae-9e48f6e42890/dqc_reference/reference_markers.fasta -out GCA_903916475.1_freshwater_MAG_---_LJ-5-9m_bin-0497_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 22:29:51,807] [INFO] Task succeeded: Blastn
[2023-06-29 22:29:51,812] [INFO] Selected 10 target genomes.
[2023-06-29 22:29:51,812] [INFO] Target genome list was writen to GCA_903916475.1_freshwater_MAG_---_LJ-5-9m_bin-0497_genomic.fna/target_genomes.txt
[2023-06-29 22:29:51,814] [INFO] Task started: fastANI
[2023-06-29 22:29:51,814] [INFO] Running command: fastANI --query /var/lib/cwl/stga28f12d1-55e7-4ff3-80f5-da7835e1a6c4/GCA_903916475.1_freshwater_MAG_---_LJ-5-9m_bin-0497_genomic.fna.gz --refList GCA_903916475.1_freshwater_MAG_---_LJ-5-9m_bin-0497_genomic.fna/target_genomes.txt --output GCA_903916475.1_freshwater_MAG_---_LJ-5-9m_bin-0497_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 22:29:56,444] [INFO] Task succeeded: fastANI
[2023-06-29 22:29:56,444] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1aeddec5-4642-4b47-84ae-9e48f6e42890/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 22:29:56,445] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1aeddec5-4642-4b47-84ae-9e48f6e42890/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 22:29:56,450] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 22:29:56,450] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 22:29:56,450] [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	82.125	185	295	95	below_threshold
Chlorobium phaeobacteroides	strain=DSM 266	GCA_000015125.1	1096	1096	type	True	78.7611	51	295	95	below_threshold
Chlorobium ferrooxidans	strain=DSM 13031	GCA_000168715.1	84205	84205	type	True	78.132	85	295	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 22:29:56,452] [INFO] DFAST Taxonomy check result was written to GCA_903916475.1_freshwater_MAG_---_LJ-5-9m_bin-0497_genomic.fna/tc_result.tsv
[2023-06-29 22:29:56,452] [INFO] ===== Taxonomy check completed =====
[2023-06-29 22:29:56,452] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 22:29:56,453] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1aeddec5-4642-4b47-84ae-9e48f6e42890/dqc_reference/checkm_data
[2023-06-29 22:29:56,454] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 22:29:56,482] [INFO] Task started: CheckM
[2023-06-29 22:29:56,482] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903916475.1_freshwater_MAG_---_LJ-5-9m_bin-0497_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903916475.1_freshwater_MAG_---_LJ-5-9m_bin-0497_genomic.fna/checkm_input GCA_903916475.1_freshwater_MAG_---_LJ-5-9m_bin-0497_genomic.fna/checkm_result
[2023-06-29 22:30:18,924] [INFO] Task succeeded: CheckM
[2023-06-29 22:30:18,925] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 60.65%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-29 22:30:18,950] [INFO] ===== Completeness check finished =====
[2023-06-29 22:30:18,951] [INFO] ===== Start GTDB Search =====
[2023-06-29 22:30:18,952] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903916475.1_freshwater_MAG_---_LJ-5-9m_bin-0497_genomic.fna/markers.fasta)
[2023-06-29 22:30:18,952] [INFO] Task started: Blastn
[2023-06-29 22:30:18,952] [INFO] Running command: blastn -query GCA_903916475.1_freshwater_MAG_---_LJ-5-9m_bin-0497_genomic.fna/markers.fasta -db /var/lib/cwl/stg1aeddec5-4642-4b47-84ae-9e48f6e42890/dqc_reference/reference_markers_gtdb.fasta -out GCA_903916475.1_freshwater_MAG_---_LJ-5-9m_bin-0497_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 22:30:19,468] [INFO] Task succeeded: Blastn
[2023-06-29 22:30:19,474] [INFO] Selected 10 target genomes.
[2023-06-29 22:30:19,474] [INFO] Target genome list was writen to GCA_903916475.1_freshwater_MAG_---_LJ-5-9m_bin-0497_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 22:30:19,477] [INFO] Task started: fastANI
[2023-06-29 22:30:19,477] [INFO] Running command: fastANI --query /var/lib/cwl/stga28f12d1-55e7-4ff3-80f5-da7835e1a6c4/GCA_903916475.1_freshwater_MAG_---_LJ-5-9m_bin-0497_genomic.fna.gz --refList GCA_903916475.1_freshwater_MAG_---_LJ-5-9m_bin-0497_genomic.fna/target_genomes_gtdb.txt --output GCA_903916475.1_freshwater_MAG_---_LJ-5-9m_bin-0497_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 22:30:24,115] [INFO] Task succeeded: fastANI
[2023-06-29 22:30:24,131] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 22:30:24,131] [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_903851535.1	s__Chlorobium sp903851535	98.1507	200	295	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.27	98.97	0.76	0.73	4	conclusive
GCA_903882665.1	s__Chlorobium sp903882665	88.6122	217	295	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.16	98.83	0.90	0.84	7	-
GCA_903840935.1	s__Chlorobium sp903840935	88.2822	184	295	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.22	98.87	0.67	0.63	5	-
GCA_903824295.1	s__Chlorobium sp903824295	85.7481	216	295	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.79	99.65	0.92	0.89	3	-
GCA_903871235.1	s__Chlorobium sp903871235	85.3029	219	295	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.74	99.66	0.91	0.89	5	-
GCA_903939765.1	s__Chlorobium sp903939765	85.1385	218	295	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.90	99.86	0.94	0.94	3	-
GCA_903917955.1	s__Chlorobium sp903917955	84.9689	165	295	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.38	99.38	0.85	0.85	2	-
GCA_903838025.1	s__Chlorobium sp903838025	83.7923	174	295	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903822595.1	s__Chlorobium sp903822595	83.3664	215	295	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.84	99.77	0.94	0.93	3	-
GCA_903865705.1	s__Chlorobium sp903865705	81.9224	164	295	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.47	99.06	0.91	0.87	5	-
--------------------------------------------------------------------------------
[2023-06-29 22:30:24,133] [INFO] GTDB search result was written to GCA_903916475.1_freshwater_MAG_---_LJ-5-9m_bin-0497_genomic.fna/result_gtdb.tsv
[2023-06-29 22:30:24,134] [INFO] ===== GTDB Search completed =====
[2023-06-29 22:30:24,137] [INFO] DFAST_QC result json was written to GCA_903916475.1_freshwater_MAG_---_LJ-5-9m_bin-0497_genomic.fna/dqc_result.json
[2023-06-29 22:30:24,137] [INFO] DFAST_QC completed!
[2023-06-29 22:30:24,137] [INFO] Total running time: 0h0m39s