[2023-06-17 16:42:55,249] [INFO] DFAST_QC pipeline started.
[2023-06-17 16:42:55,252] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 16:42:55,252] [INFO] DQC Reference Directory: /var/lib/cwl/stge779764f-3453-425f-b641-2362246ad71f/dqc_reference
[2023-06-17 16:42:56,614] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 16:42:56,615] [INFO] Task started: Prodigal
[2023-06-17 16:42:56,615] [INFO] Running command: gunzip -c /var/lib/cwl/stg24afbe2c-ecd5-4341-8ed2-1f9e1b5bcb32/GCA_905207255.1_ERR260195-mag-bin.1_genomic.fna.gz | prodigal -d GCA_905207255.1_ERR260195-mag-bin.1_genomic.fna/cds.fna -a GCA_905207255.1_ERR260195-mag-bin.1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 16:43:00,295] [INFO] Task succeeded: Prodigal
[2023-06-17 16:43:00,296] [INFO] Task started: HMMsearch
[2023-06-17 16:43:00,296] [INFO] Running command: hmmsearch --tblout GCA_905207255.1_ERR260195-mag-bin.1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge779764f-3453-425f-b641-2362246ad71f/dqc_reference/reference_markers.hmm GCA_905207255.1_ERR260195-mag-bin.1_genomic.fna/protein.faa > /dev/null
[2023-06-17 16:43:00,512] [INFO] Task succeeded: HMMsearch
[2023-06-17 16:43:00,515] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg24afbe2c-ecd5-4341-8ed2-1f9e1b5bcb32/GCA_905207255.1_ERR260195-mag-bin.1_genomic.fna.gz]
[2023-06-17 16:43:00,540] [INFO] Query marker FASTA was written to GCA_905207255.1_ERR260195-mag-bin.1_genomic.fna/markers.fasta
[2023-06-17 16:43:00,540] [INFO] Task started: Blastn
[2023-06-17 16:43:00,540] [INFO] Running command: blastn -query GCA_905207255.1_ERR260195-mag-bin.1_genomic.fna/markers.fasta -db /var/lib/cwl/stge779764f-3453-425f-b641-2362246ad71f/dqc_reference/reference_markers.fasta -out GCA_905207255.1_ERR260195-mag-bin.1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 16:43:01,161] [INFO] Task succeeded: Blastn
[2023-06-17 16:43:01,166] [INFO] Selected 20 target genomes.
[2023-06-17 16:43:01,167] [INFO] Target genome list was writen to GCA_905207255.1_ERR260195-mag-bin.1_genomic.fna/target_genomes.txt
[2023-06-17 16:43:01,179] [INFO] Task started: fastANI
[2023-06-17 16:43:01,180] [INFO] Running command: fastANI --query /var/lib/cwl/stg24afbe2c-ecd5-4341-8ed2-1f9e1b5bcb32/GCA_905207255.1_ERR260195-mag-bin.1_genomic.fna.gz --refList GCA_905207255.1_ERR260195-mag-bin.1_genomic.fna/target_genomes.txt --output GCA_905207255.1_ERR260195-mag-bin.1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 16:43:12,897] [INFO] Task succeeded: fastANI
[2023-06-17 16:43:12,898] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge779764f-3453-425f-b641-2362246ad71f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 16:43:12,898] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge779764f-3453-425f-b641-2362246ad71f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 16:43:12,901] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 16:43:12,902] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 16:43:12,902] [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
--------------------------------------------------------------------------------
[2023-06-17 16:43:12,905] [INFO] DFAST Taxonomy check result was written to GCA_905207255.1_ERR260195-mag-bin.1_genomic.fna/tc_result.tsv
[2023-06-17 16:43:12,905] [INFO] ===== Taxonomy check completed =====
[2023-06-17 16:43:12,906] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 16:43:12,906] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge779764f-3453-425f-b641-2362246ad71f/dqc_reference/checkm_data
[2023-06-17 16:43:12,909] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 16:43:12,930] [INFO] Task started: CheckM
[2023-06-17 16:43:12,930] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_905207255.1_ERR260195-mag-bin.1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_905207255.1_ERR260195-mag-bin.1_genomic.fna/checkm_input GCA_905207255.1_ERR260195-mag-bin.1_genomic.fna/checkm_result
[2023-06-17 16:43:31,470] [INFO] Task succeeded: CheckM
[2023-06-17 16:43:31,471] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.88%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 16:43:31,497] [INFO] ===== Completeness check finished =====
[2023-06-17 16:43:31,498] [INFO] ===== Start GTDB Search =====
[2023-06-17 16:43:31,498] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_905207255.1_ERR260195-mag-bin.1_genomic.fna/markers.fasta)
[2023-06-17 16:43:31,498] [INFO] Task started: Blastn
[2023-06-17 16:43:31,499] [INFO] Running command: blastn -query GCA_905207255.1_ERR260195-mag-bin.1_genomic.fna/markers.fasta -db /var/lib/cwl/stge779764f-3453-425f-b641-2362246ad71f/dqc_reference/reference_markers_gtdb.fasta -out GCA_905207255.1_ERR260195-mag-bin.1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 16:43:32,429] [INFO] Task succeeded: Blastn
[2023-06-17 16:43:32,435] [INFO] Selected 23 target genomes.
[2023-06-17 16:43:32,435] [INFO] Target genome list was writen to GCA_905207255.1_ERR260195-mag-bin.1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 16:43:32,468] [INFO] Task started: fastANI
[2023-06-17 16:43:32,469] [INFO] Running command: fastANI --query /var/lib/cwl/stg24afbe2c-ecd5-4341-8ed2-1f9e1b5bcb32/GCA_905207255.1_ERR260195-mag-bin.1_genomic.fna.gz --refList GCA_905207255.1_ERR260195-mag-bin.1_genomic.fna/target_genomes_gtdb.txt --output GCA_905207255.1_ERR260195-mag-bin.1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 16:43:39,959] [INFO] Task succeeded: fastANI
[2023-06-17 16:43:39,969] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-17 16:43:39,969] [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_900549865.1	s__Limivicinus sp900549865	79.9714	100	219	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	98.13	98.09	0.79	0.79	3	-
GCA_900549545.1	s__Limivicinus sp900549545	79.3005	68	219	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	99.92	99.84	0.93	0.88	3	-
GCA_900546515.1	s__Limivicinus sp900546515	79.0617	110	219	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	99.98	99.98	0.95	0.95	2	-
GCA_002431965.1	s__Limivicinus sp002431965	78.9867	101	219	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	99.06	98.60	0.95	0.94	5	-
GCA_900547315.1	s__Limivicinus sp900547315	78.5766	72	219	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	98.47	98.42	0.88	0.83	3	-
GCA_900549645.1	s__Limivicinus sp900549645	78.3377	71	219	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	99.52	99.05	0.92	0.86	3	-
GCA_905233785.1	s__Limivicinus sp905233785	77.6398	61	219	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Oscillospiraceae;g__Limivicinus	95.0	98.68	98.68	0.83	0.83	2	-
--------------------------------------------------------------------------------
[2023-06-17 16:43:39,971] [INFO] GTDB search result was written to GCA_905207255.1_ERR260195-mag-bin.1_genomic.fna/result_gtdb.tsv
[2023-06-17 16:43:39,972] [INFO] ===== GTDB Search completed =====
[2023-06-17 16:43:39,978] [INFO] DFAST_QC result json was written to GCA_905207255.1_ERR260195-mag-bin.1_genomic.fna/dqc_result.json
[2023-06-17 16:43:39,978] [INFO] DFAST_QC completed!
[2023-06-17 16:43:39,978] [INFO] Total running time: 0h0m45s