[2023-07-01 01:02:17,754] [INFO] DFAST_QC pipeline started.
[2023-07-01 01:02:17,756] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 01:02:17,757] [INFO] DQC Reference Directory: /var/lib/cwl/stg402ac788-30dd-49d2-8315-eeec91b90599/dqc_reference
[2023-07-01 01:02:20,134] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 01:02:20,135] [INFO] Task started: Prodigal
[2023-07-01 01:02:20,136] [INFO] Running command: gunzip -c /var/lib/cwl/stgaf745dc4-6477-48a6-ad52-8f95ac495c1f/GCA_903866925.1_freshwater_MAG_---_AM-lipid-01-D6_bin-356_genomic.fna.gz | prodigal -d GCA_903866925.1_freshwater_MAG_---_AM-lipid-01-D6_bin-356_genomic.fna/cds.fna -a GCA_903866925.1_freshwater_MAG_---_AM-lipid-01-D6_bin-356_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 01:02:26,484] [INFO] Task succeeded: Prodigal
[2023-07-01 01:02:26,484] [INFO] Task started: HMMsearch
[2023-07-01 01:02:26,484] [INFO] Running command: hmmsearch --tblout GCA_903866925.1_freshwater_MAG_---_AM-lipid-01-D6_bin-356_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg402ac788-30dd-49d2-8315-eeec91b90599/dqc_reference/reference_markers.hmm GCA_903866925.1_freshwater_MAG_---_AM-lipid-01-D6_bin-356_genomic.fna/protein.faa > /dev/null
[2023-07-01 01:02:26,666] [INFO] Task succeeded: HMMsearch
[2023-07-01 01:02:26,668] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgaf745dc4-6477-48a6-ad52-8f95ac495c1f/GCA_903866925.1_freshwater_MAG_---_AM-lipid-01-D6_bin-356_genomic.fna.gz]
[2023-07-01 01:02:26,687] [INFO] Query marker FASTA was written to GCA_903866925.1_freshwater_MAG_---_AM-lipid-01-D6_bin-356_genomic.fna/markers.fasta
[2023-07-01 01:02:26,687] [INFO] Task started: Blastn
[2023-07-01 01:02:26,687] [INFO] Running command: blastn -query GCA_903866925.1_freshwater_MAG_---_AM-lipid-01-D6_bin-356_genomic.fna/markers.fasta -db /var/lib/cwl/stg402ac788-30dd-49d2-8315-eeec91b90599/dqc_reference/reference_markers.fasta -out GCA_903866925.1_freshwater_MAG_---_AM-lipid-01-D6_bin-356_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 01:02:27,182] [INFO] Task succeeded: Blastn
[2023-07-01 01:02:27,186] [INFO] Selected 9 target genomes.
[2023-07-01 01:02:27,186] [INFO] Target genome list was writen to GCA_903866925.1_freshwater_MAG_---_AM-lipid-01-D6_bin-356_genomic.fna/target_genomes.txt
[2023-07-01 01:02:27,189] [INFO] Task started: fastANI
[2023-07-01 01:02:27,189] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf745dc4-6477-48a6-ad52-8f95ac495c1f/GCA_903866925.1_freshwater_MAG_---_AM-lipid-01-D6_bin-356_genomic.fna.gz --refList GCA_903866925.1_freshwater_MAG_---_AM-lipid-01-D6_bin-356_genomic.fna/target_genomes.txt --output GCA_903866925.1_freshwater_MAG_---_AM-lipid-01-D6_bin-356_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 01:02:31,509] [INFO] Task succeeded: fastANI
[2023-07-01 01:02:31,509] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg402ac788-30dd-49d2-8315-eeec91b90599/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 01:02:31,510] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg402ac788-30dd-49d2-8315-eeec91b90599/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 01:02:31,518] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 01:02:31,518] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-07-01 01:02:31,519] [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	77.7519	132	354	95	below_threshold
Chlorobium ferrooxidans	strain=DSM 13031	GCA_000168715.1	84205	84205	type	True	77.6094	117	354	95	below_threshold
Chlorobium phaeobacteroides	strain=DSM 266	GCA_000015125.1	1096	1096	type	True	76.6462	67	354	95	below_threshold
--------------------------------------------------------------------------------
[2023-07-01 01:02:31,520] [INFO] DFAST Taxonomy check result was written to GCA_903866925.1_freshwater_MAG_---_AM-lipid-01-D6_bin-356_genomic.fna/tc_result.tsv
[2023-07-01 01:02:31,521] [INFO] ===== Taxonomy check completed =====
[2023-07-01 01:02:31,521] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 01:02:31,521] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg402ac788-30dd-49d2-8315-eeec91b90599/dqc_reference/checkm_data
[2023-07-01 01:02:31,522] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 01:02:31,543] [INFO] Task started: CheckM
[2023-07-01 01:02:31,543] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903866925.1_freshwater_MAG_---_AM-lipid-01-D6_bin-356_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903866925.1_freshwater_MAG_---_AM-lipid-01-D6_bin-356_genomic.fna/checkm_input GCA_903866925.1_freshwater_MAG_---_AM-lipid-01-D6_bin-356_genomic.fna/checkm_result
[2023-07-01 01:02:57,178] [INFO] Task succeeded: CheckM
[2023-07-01 01:02:57,180] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 22.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-07-01 01:02:57,199] [INFO] ===== Completeness check finished =====
[2023-07-01 01:02:57,200] [INFO] ===== Start GTDB Search =====
[2023-07-01 01:02:57,200] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903866925.1_freshwater_MAG_---_AM-lipid-01-D6_bin-356_genomic.fna/markers.fasta)
[2023-07-01 01:02:57,201] [INFO] Task started: Blastn
[2023-07-01 01:02:57,201] [INFO] Running command: blastn -query GCA_903866925.1_freshwater_MAG_---_AM-lipid-01-D6_bin-356_genomic.fna/markers.fasta -db /var/lib/cwl/stg402ac788-30dd-49d2-8315-eeec91b90599/dqc_reference/reference_markers_gtdb.fasta -out GCA_903866925.1_freshwater_MAG_---_AM-lipid-01-D6_bin-356_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 01:02:57,677] [INFO] Task succeeded: Blastn
[2023-07-01 01:02:57,681] [INFO] Selected 7 target genomes.
[2023-07-01 01:02:57,681] [INFO] Target genome list was writen to GCA_903866925.1_freshwater_MAG_---_AM-lipid-01-D6_bin-356_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 01:02:57,682] [INFO] Task started: fastANI
[2023-07-01 01:02:57,682] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf745dc4-6477-48a6-ad52-8f95ac495c1f/GCA_903866925.1_freshwater_MAG_---_AM-lipid-01-D6_bin-356_genomic.fna.gz --refList GCA_903866925.1_freshwater_MAG_---_AM-lipid-01-D6_bin-356_genomic.fna/target_genomes_gtdb.txt --output GCA_903866925.1_freshwater_MAG_---_AM-lipid-01-D6_bin-356_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 01:03:00,922] [INFO] Task succeeded: fastANI
[2023-07-01 01:03:00,939] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-07-01 01:03:00,940] [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_903895195.1	s__Chlorobium sp903895195	99.2886	346	354	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.16	98.65	0.92	0.86	65	conclusive
GCA_005843825.1	s__Chlorobium sp005843825	87.3774	303	354	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	98.19	97.55	0.89	0.82	50	-
GCA_903908555.1	s__Chlorobium sp903908555	87.1675	254	354	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.53	99.53	0.79	0.79	2	-
GCA_903851385.1	s__Chlorobium sp903851385	87.15	306	354	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.86	99.82	0.97	0.97	3	-
GCA_903920215.1	s__Chlorobium sp903920215	86.8053	287	354	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903904495.1	s__Chlorobium sp903904495	82.8202	212	354	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	98.87	98.87	0.74	0.74	2	-
GCA_012972835.1	s__Chlorobium sp012972835	80.2697	243	354	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-07-01 01:03:00,946] [INFO] GTDB search result was written to GCA_903866925.1_freshwater_MAG_---_AM-lipid-01-D6_bin-356_genomic.fna/result_gtdb.tsv
[2023-07-01 01:03:00,948] [INFO] ===== GTDB Search completed =====
[2023-07-01 01:03:00,954] [INFO] DFAST_QC result json was written to GCA_903866925.1_freshwater_MAG_---_AM-lipid-01-D6_bin-356_genomic.fna/dqc_result.json
[2023-07-01 01:03:00,955] [INFO] DFAST_QC completed!
[2023-07-01 01:03:00,955] [INFO] Total running time: 0h0m43s