[2023-06-19 05:24:41,851] [INFO] DFAST_QC pipeline started.
[2023-06-19 05:24:41,855] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 05:24:41,855] [INFO] DQC Reference Directory: /var/lib/cwl/stgbe4774c0-e826-4406-aa03-27c57d377b30/dqc_reference
[2023-06-19 05:24:43,257] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 05:24:43,260] [INFO] Task started: Prodigal
[2023-06-19 05:24:43,260] [INFO] Running command: gunzip -c /var/lib/cwl/stg3b5f6173-7cad-4506-ae44-c73d871f83a7/GCA_937895545.1_ERR4757842_bin.16_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937895545.1_ERR4757842_bin.16_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937895545.1_ERR4757842_bin.16_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 05:24:52,129] [INFO] Task succeeded: Prodigal
[2023-06-19 05:24:52,129] [INFO] Task started: HMMsearch
[2023-06-19 05:24:52,129] [INFO] Running command: hmmsearch --tblout GCA_937895545.1_ERR4757842_bin.16_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbe4774c0-e826-4406-aa03-27c57d377b30/dqc_reference/reference_markers.hmm GCA_937895545.1_ERR4757842_bin.16_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-19 05:24:52,424] [INFO] Task succeeded: HMMsearch
[2023-06-19 05:24:52,428] [INFO] Found 6/6 markers.
[2023-06-19 05:24:52,468] [INFO] Query marker FASTA was written to GCA_937895545.1_ERR4757842_bin.16_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-19 05:24:52,469] [INFO] Task started: Blastn
[2023-06-19 05:24:52,469] [INFO] Running command: blastn -query GCA_937895545.1_ERR4757842_bin.16_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe4774c0-e826-4406-aa03-27c57d377b30/dqc_reference/reference_markers.fasta -out GCA_937895545.1_ERR4757842_bin.16_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 05:24:53,256] [INFO] Task succeeded: Blastn
[2023-06-19 05:24:53,261] [INFO] Selected 11 target genomes.
[2023-06-19 05:24:53,261] [INFO] Target genome list was writen to GCA_937895545.1_ERR4757842_bin.16_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-19 05:24:53,265] [INFO] Task started: fastANI
[2023-06-19 05:24:53,265] [INFO] Running command: fastANI --query /var/lib/cwl/stg3b5f6173-7cad-4506-ae44-c73d871f83a7/GCA_937895545.1_ERR4757842_bin.16_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937895545.1_ERR4757842_bin.16_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_937895545.1_ERR4757842_bin.16_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 05:25:01,424] [INFO] Task succeeded: fastANI
[2023-06-19 05:25:01,424] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbe4774c0-e826-4406-aa03-27c57d377b30/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 05:25:01,424] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbe4774c0-e826-4406-aa03-27c57d377b30/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 05:25:01,431] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2023-06-19 05:25:01,431] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-19 05:25:01,432] [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
Acetobacter malorum	strain=LMG 1746	GCA_001580615.1	178901	178901	suspected-type	True	96.1581	867	939	95	conclusive
Acetobacter cerevisiae	strain=LMG 1625	GCA_001580535.1	178900	178900	type	True	93.2477	764	939	95	below_threshold
Acetobacter persici	strain=JCM 25330	GCA_000613905.1	1076596	1076596	type	True	85.8555	707	939	95	below_threshold
Acetobacter orleanensis	strain=LMG 1583	GCA_001581005.1	104099	104099	type	True	85.0288	673	939	95	below_threshold
Acetobacter orleanensis	strain=NBRC 13752	GCA_006539325.1	104099	104099	type	True	84.9784	668	939	95	below_threshold
Acetobacter orleanensis	strain=JCM 7639T	GCA_000964205.1	104099	104099	type	True	84.9452	668	939	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 05:25:01,434] [INFO] DFAST Taxonomy check result was written to GCA_937895545.1_ERR4757842_bin.16_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-19 05:25:01,435] [INFO] ===== Taxonomy check completed =====
[2023-06-19 05:25:01,435] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 05:25:01,435] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbe4774c0-e826-4406-aa03-27c57d377b30/dqc_reference/checkm_data
[2023-06-19 05:25:01,437] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 05:25:01,479] [INFO] Task started: CheckM
[2023-06-19 05:25:01,479] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937895545.1_ERR4757842_bin.16_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937895545.1_ERR4757842_bin.16_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937895545.1_ERR4757842_bin.16_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-19 05:25:32,907] [INFO] Task succeeded: CheckM
[2023-06-19 05:25:32,909] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 05:25:32,945] [INFO] ===== Completeness check finished =====
[2023-06-19 05:25:32,945] [INFO] ===== Start GTDB Search =====
[2023-06-19 05:25:32,945] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937895545.1_ERR4757842_bin.16_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-19 05:25:32,946] [INFO] Task started: Blastn
[2023-06-19 05:25:32,946] [INFO] Running command: blastn -query GCA_937895545.1_ERR4757842_bin.16_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe4774c0-e826-4406-aa03-27c57d377b30/dqc_reference/reference_markers_gtdb.fasta -out GCA_937895545.1_ERR4757842_bin.16_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 05:25:34,138] [INFO] Task succeeded: Blastn
[2023-06-19 05:25:34,143] [INFO] Selected 7 target genomes.
[2023-06-19 05:25:34,144] [INFO] Target genome list was writen to GCA_937895545.1_ERR4757842_bin.16_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 05:25:34,151] [INFO] Task started: fastANI
[2023-06-19 05:25:34,152] [INFO] Running command: fastANI --query /var/lib/cwl/stg3b5f6173-7cad-4506-ae44-c73d871f83a7/GCA_937895545.1_ERR4757842_bin.16_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937895545.1_ERR4757842_bin.16_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937895545.1_ERR4757842_bin.16_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 05:25:39,372] [INFO] Task succeeded: fastANI
[2023-06-19 05:25:39,393] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 05:25:39,393] [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_001580615.1	s__Acetobacter malorum	96.1581	867	939	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	95.98	95.83	0.82	0.80	5	conclusive
GCF_001580535.1	s__Acetobacter cerevisiae	93.2477	764	939	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	96.52	96.47	0.88	0.86	4	-
GCF_002153605.1	s__Acetobacter malorum_A	90.8305	754	939	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	96.53	96.53	0.89	0.89	2	-
GCF_000613905.1	s__Acetobacter persici	85.8651	706	939	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	96.00	95.85	0.80	0.79	8	-
GCF_001581005.1	s__Acetobacter orleanensis	85.0288	673	939	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	99.99	99.99	0.99	0.99	4	-
GCF_011516935.1	s__Acetobacter farinalis	83.9829	636	939	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001580995.1	s__Acetobacter senegalensis	80.732	492	939	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	97.25	96.97	0.85	0.80	6	-
--------------------------------------------------------------------------------
[2023-06-19 05:25:39,395] [INFO] GTDB search result was written to GCA_937895545.1_ERR4757842_bin.16_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-19 05:25:39,396] [INFO] ===== GTDB Search completed =====
[2023-06-19 05:25:39,401] [INFO] DFAST_QC result json was written to GCA_937895545.1_ERR4757842_bin.16_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-19 05:25:39,401] [INFO] DFAST_QC completed!
[2023-06-19 05:25:39,401] [INFO] Total running time: 0h0m58s