[2023-06-13 19:38:48,944] [INFO] DFAST_QC pipeline started.
[2023-06-13 19:38:48,946] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 19:38:48,946] [INFO] DQC Reference Directory: /var/lib/cwl/stg0a916cbe-6800-4a40-8593-ac13197a415f/dqc_reference
[2023-06-13 19:38:50,132] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 19:38:50,133] [INFO] Task started: Prodigal
[2023-06-13 19:38:50,133] [INFO] Running command: gunzip -c /var/lib/cwl/stg2ca4b4ca-2171-47ae-a656-39e6d775b950/GCA_022562995.1_ASM2256299v1_genomic.fna.gz | prodigal -d GCA_022562995.1_ASM2256299v1_genomic.fna/cds.fna -a GCA_022562995.1_ASM2256299v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 19:38:55,317] [INFO] Task succeeded: Prodigal
[2023-06-13 19:38:55,317] [INFO] Task started: HMMsearch
[2023-06-13 19:38:55,317] [INFO] Running command: hmmsearch --tblout GCA_022562995.1_ASM2256299v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0a916cbe-6800-4a40-8593-ac13197a415f/dqc_reference/reference_markers.hmm GCA_022562995.1_ASM2256299v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 19:38:55,509] [INFO] Task succeeded: HMMsearch
[2023-06-13 19:38:55,511] [INFO] Found 6/6 markers.
[2023-06-13 19:38:55,531] [INFO] Query marker FASTA was written to GCA_022562995.1_ASM2256299v1_genomic.fna/markers.fasta
[2023-06-13 19:38:55,532] [INFO] Task started: Blastn
[2023-06-13 19:38:55,532] [INFO] Running command: blastn -query GCA_022562995.1_ASM2256299v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0a916cbe-6800-4a40-8593-ac13197a415f/dqc_reference/reference_markers.fasta -out GCA_022562995.1_ASM2256299v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 19:38:56,231] [INFO] Task succeeded: Blastn
[2023-06-13 19:38:56,235] [INFO] Selected 40 target genomes.
[2023-06-13 19:38:56,235] [INFO] Target genome list was writen to GCA_022562995.1_ASM2256299v1_genomic.fna/target_genomes.txt
[2023-06-13 19:38:56,238] [INFO] Task started: fastANI
[2023-06-13 19:38:56,238] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ca4b4ca-2171-47ae-a656-39e6d775b950/GCA_022562995.1_ASM2256299v1_genomic.fna.gz --refList GCA_022562995.1_ASM2256299v1_genomic.fna/target_genomes.txt --output GCA_022562995.1_ASM2256299v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 19:39:19,837] [INFO] Task succeeded: fastANI
[2023-06-13 19:39:19,838] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0a916cbe-6800-4a40-8593-ac13197a415f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 19:39:19,838] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0a916cbe-6800-4a40-8593-ac13197a415f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 19:39:19,845] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 19:39:19,845] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 19:39:19,845] [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
Rhodothalassium salexigens	strain=DSM 2132	GCA_004341375.1	1086	1086	type	True	76.1597	57	651	95	below_threshold
Rhodothalassium salexigens	strain=DSM 2132	GCA_016583875.1	1086	1086	type	True	76.1471	56	651	95	below_threshold
Rhodothalassium salexigens	strain=DSM 2132	GCA_014197775.1	1086	1086	type	True	76.1395	56	651	95	below_threshold
Stella humosa	strain=ATCC 43930	GCA_006738645.1	94	94	type	True	75.5912	55	651	95	below_threshold
Thalassobaculum fulvum	strain=KCTC 42651	GCA_014652915.1	1633335	1633335	type	True	75.5235	57	651	95	below_threshold
Methylobacterium oryzihabitans	strain=TER-1	GCA_004004555.2	2499852	2499852	type	True	75.4968	53	651	95	below_threshold
Stella humosa	strain=DSM 5900	GCA_003751345.1	94	94	type	True	75.4908	55	651	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 19:39:19,847] [INFO] DFAST Taxonomy check result was written to GCA_022562995.1_ASM2256299v1_genomic.fna/tc_result.tsv
[2023-06-13 19:39:19,848] [INFO] ===== Taxonomy check completed =====
[2023-06-13 19:39:19,848] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 19:39:19,848] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0a916cbe-6800-4a40-8593-ac13197a415f/dqc_reference/checkm_data
[2023-06-13 19:39:19,849] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 19:39:19,871] [INFO] Task started: CheckM
[2023-06-13 19:39:19,872] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022562995.1_ASM2256299v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022562995.1_ASM2256299v1_genomic.fna/checkm_input GCA_022562995.1_ASM2256299v1_genomic.fna/checkm_result
[2023-06-13 19:39:41,220] [INFO] Task succeeded: CheckM
[2023-06-13 19:39:41,220] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.07%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 19:39:41,237] [INFO] ===== Completeness check finished =====
[2023-06-13 19:39:41,237] [INFO] ===== Start GTDB Search =====
[2023-06-13 19:39:41,237] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022562995.1_ASM2256299v1_genomic.fna/markers.fasta)
[2023-06-13 19:39:41,237] [INFO] Task started: Blastn
[2023-06-13 19:39:41,238] [INFO] Running command: blastn -query GCA_022562995.1_ASM2256299v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0a916cbe-6800-4a40-8593-ac13197a415f/dqc_reference/reference_markers_gtdb.fasta -out GCA_022562995.1_ASM2256299v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 19:39:42,342] [INFO] Task succeeded: Blastn
[2023-06-13 19:39:42,346] [INFO] Selected 36 target genomes.
[2023-06-13 19:39:42,346] [INFO] Target genome list was writen to GCA_022562995.1_ASM2256299v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 19:39:42,354] [INFO] Task started: fastANI
[2023-06-13 19:39:42,354] [INFO] Running command: fastANI --query /var/lib/cwl/stg2ca4b4ca-2171-47ae-a656-39e6d775b950/GCA_022562995.1_ASM2256299v1_genomic.fna.gz --refList GCA_022562995.1_ASM2256299v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022562995.1_ASM2256299v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 19:40:05,921] [INFO] Task succeeded: fastANI
[2023-06-13 19:40:05,927] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 19:40:05,927] [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_004356215.1	s__SMXR01 sp004356215	77.6048	102	651	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__SMXR01;g__SMXR01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004341375.1	s__Rhodothalassium salexigens	76.1597	57	651	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Rhodothalassiaceae;g__Rhodothalassium	95.0	97.98	95.92	0.96	0.92	5	-
GCA_003577275.1	s__PRO5 sp003577275	75.9504	57	651	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__J090;g__PRO5	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005938675.2	s__Inquilinus sp005938675	75.6262	52	651	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__DSM-16000;f__Inquilinaceae;g__Inquilinus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652915.1	s__Thalassobaculum_A fulvum	75.5443	56	651	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Thalassobaculales;f__Thalassobaculaceae;g__Thalassobaculum_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 19:40:05,929] [INFO] GTDB search result was written to GCA_022562995.1_ASM2256299v1_genomic.fna/result_gtdb.tsv
[2023-06-13 19:40:05,930] [INFO] ===== GTDB Search completed =====
[2023-06-13 19:40:05,933] [INFO] DFAST_QC result json was written to GCA_022562995.1_ASM2256299v1_genomic.fna/dqc_result.json
[2023-06-13 19:40:05,933] [INFO] DFAST_QC completed!
[2023-06-13 19:40:05,933] [INFO] Total running time: 0h1m17s