[2023-06-28 02:21:42,421] [INFO] DFAST_QC pipeline started.
[2023-06-28 02:21:42,425] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 02:21:42,426] [INFO] DQC Reference Directory: /var/lib/cwl/stg81bc838f-7fb7-40b2-b21e-f1a2c08dd1b7/dqc_reference
[2023-06-28 02:21:45,743] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 02:21:45,744] [INFO] Task started: Prodigal
[2023-06-28 02:21:45,744] [INFO] Running command: gunzip -c /var/lib/cwl/stg27181077-06d2-4dc6-b4ee-0d838199218a/GCA_913052485.1_ERR599050_bin.113_MetaBAT_v2.12.1_MAG_genomic.fna.gz | prodigal -d GCA_913052485.1_ERR599050_bin.113_MetaBAT_v2.12.1_MAG_genomic.fna/cds.fna -a GCA_913052485.1_ERR599050_bin.113_MetaBAT_v2.12.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 02:21:48,993] [INFO] Task succeeded: Prodigal
[2023-06-28 02:21:48,994] [INFO] Task started: HMMsearch
[2023-06-28 02:21:48,994] [INFO] Running command: hmmsearch --tblout GCA_913052485.1_ERR599050_bin.113_MetaBAT_v2.12.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg81bc838f-7fb7-40b2-b21e-f1a2c08dd1b7/dqc_reference/reference_markers.hmm GCA_913052485.1_ERR599050_bin.113_MetaBAT_v2.12.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-28 02:21:49,256] [INFO] Task succeeded: HMMsearch
[2023-06-28 02:21:49,258] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg27181077-06d2-4dc6-b4ee-0d838199218a/GCA_913052485.1_ERR599050_bin.113_MetaBAT_v2.12.1_MAG_genomic.fna.gz]
[2023-06-28 02:21:49,281] [INFO] Query marker FASTA was written to GCA_913052485.1_ERR599050_bin.113_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta
[2023-06-28 02:21:49,282] [INFO] Task started: Blastn
[2023-06-28 02:21:49,282] [INFO] Running command: blastn -query GCA_913052485.1_ERR599050_bin.113_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg81bc838f-7fb7-40b2-b21e-f1a2c08dd1b7/dqc_reference/reference_markers.fasta -out GCA_913052485.1_ERR599050_bin.113_MetaBAT_v2.12.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 02:21:50,845] [INFO] Task succeeded: Blastn
[2023-06-28 02:21:50,849] [INFO] Selected 20 target genomes.
[2023-06-28 02:21:50,849] [INFO] Target genome list was writen to GCA_913052485.1_ERR599050_bin.113_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes.txt
[2023-06-28 02:21:50,851] [INFO] Task started: fastANI
[2023-06-28 02:21:50,851] [INFO] Running command: fastANI --query /var/lib/cwl/stg27181077-06d2-4dc6-b4ee-0d838199218a/GCA_913052485.1_ERR599050_bin.113_MetaBAT_v2.12.1_MAG_genomic.fna.gz --refList GCA_913052485.1_ERR599050_bin.113_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes.txt --output GCA_913052485.1_ERR599050_bin.113_MetaBAT_v2.12.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 02:21:59,489] [INFO] Task succeeded: fastANI
[2023-06-28 02:21:59,489] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg81bc838f-7fb7-40b2-b21e-f1a2c08dd1b7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 02:21:59,490] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg81bc838f-7fb7-40b2-b21e-f1a2c08dd1b7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 02:21:59,492] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 02:21:59,492] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 02:21:59,492] [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
--------------------------------------------------------------------------------
[2023-06-28 02:21:59,495] [INFO] DFAST Taxonomy check result was written to GCA_913052485.1_ERR599050_bin.113_MetaBAT_v2.12.1_MAG_genomic.fna/tc_result.tsv
[2023-06-28 02:21:59,496] [INFO] ===== Taxonomy check completed =====
[2023-06-28 02:21:59,497] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 02:21:59,497] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg81bc838f-7fb7-40b2-b21e-f1a2c08dd1b7/dqc_reference/checkm_data
[2023-06-28 02:21:59,502] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 02:21:59,526] [INFO] Task started: CheckM
[2023-06-28 02:21:59,526] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_913052485.1_ERR599050_bin.113_MetaBAT_v2.12.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_913052485.1_ERR599050_bin.113_MetaBAT_v2.12.1_MAG_genomic.fna/checkm_input GCA_913052485.1_ERR599050_bin.113_MetaBAT_v2.12.1_MAG_genomic.fna/checkm_result
[2023-06-28 02:22:16,928] [INFO] Task succeeded: CheckM
[2023-06-28 02:22:16,929] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 02:22:16,951] [INFO] ===== Completeness check finished =====
[2023-06-28 02:22:16,951] [INFO] ===== Start GTDB Search =====
[2023-06-28 02:22:16,952] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_913052485.1_ERR599050_bin.113_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta)
[2023-06-28 02:22:16,952] [INFO] Task started: Blastn
[2023-06-28 02:22:16,952] [INFO] Running command: blastn -query GCA_913052485.1_ERR599050_bin.113_MetaBAT_v2.12.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg81bc838f-7fb7-40b2-b21e-f1a2c08dd1b7/dqc_reference/reference_markers_gtdb.fasta -out GCA_913052485.1_ERR599050_bin.113_MetaBAT_v2.12.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 02:22:18,056] [INFO] Task succeeded: Blastn
[2023-06-28 02:22:18,061] [INFO] Selected 23 target genomes.
[2023-06-28 02:22:18,061] [INFO] Target genome list was writen to GCA_913052485.1_ERR599050_bin.113_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 02:22:18,100] [INFO] Task started: fastANI
[2023-06-28 02:22:18,101] [INFO] Running command: fastANI --query /var/lib/cwl/stg27181077-06d2-4dc6-b4ee-0d838199218a/GCA_913052485.1_ERR599050_bin.113_MetaBAT_v2.12.1_MAG_genomic.fna.gz --refList GCA_913052485.1_ERR599050_bin.113_MetaBAT_v2.12.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_913052485.1_ERR599050_bin.113_MetaBAT_v2.12.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 02:22:24,199] [INFO] Task succeeded: fastANI
[2023-06-28 02:22:24,213] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 02:22:24,213] [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_902626505.1	s__MED-G16 sp902626505	80.1958	214	386	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__MED-G16;g__MED-G16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002701745.1	s__MED-G16 sp002701745	79.9583	133	386	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__MED-G16;g__MED-G16	95.0	96.78	96.78	0.79	0.79	2	-
GCA_902634135.1	s__MED-G16 sp902634135	79.3766	138	386	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__MED-G16;g__MED-G16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002697405.1	s__MED-G16 sp002697405	78.1152	143	386	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__MED-G16;g__MED-G16	95.0	98.03	98.03	0.62	0.62	2	-
GCA_002696995.1	s__MED-G16 sp002696995	77.9642	108	386	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__MED-G16;g__MED-G16	95.0	95.99	95.99	0.74	0.74	2	-
GCA_902523065.1	s__MED-G16 sp902523065	77.8602	95	386	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__MED-G16;g__MED-G16	95.0	96.84	95.61	0.92	0.88	9	-
GCA_902633975.1	s__MED-G16 sp902633975	77.8109	74	386	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__MED-G16;g__MED-G16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002692105.1	s__MED-G16 sp002692105	77.5993	94	386	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__MED-G16;g__MED-G16	95.0	97.44	97.02	0.77	0.72	3	-
GCA_002457315.1	s__MED-G16 sp002457315	77.359	145	386	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__MED-G16;g__MED-G16	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 02:22:24,216] [INFO] GTDB search result was written to GCA_913052485.1_ERR599050_bin.113_MetaBAT_v2.12.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-28 02:22:24,217] [INFO] ===== GTDB Search completed =====
[2023-06-28 02:22:24,223] [INFO] DFAST_QC result json was written to GCA_913052485.1_ERR599050_bin.113_MetaBAT_v2.12.1_MAG_genomic.fna/dqc_result.json
[2023-06-28 02:22:24,224] [INFO] DFAST_QC completed!
[2023-06-28 02:22:24,224] [INFO] Total running time: 0h0m42s