[2023-06-19 13:54:08,957] [INFO] DFAST_QC pipeline started.
[2023-06-19 13:54:08,959] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 13:54:08,960] [INFO] DQC Reference Directory: /var/lib/cwl/stg5442acf4-f3b8-4bcc-974a-dac211211e83/dqc_reference
[2023-06-19 13:54:10,274] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 13:54:10,275] [INFO] Task started: Prodigal
[2023-06-19 13:54:10,275] [INFO] Running command: gunzip -c /var/lib/cwl/stg9ca9eb18-a022-480f-ba54-732d8c70388c/GCA_018971005.1_ASM1897100v1_genomic.fna.gz | prodigal -d GCA_018971005.1_ASM1897100v1_genomic.fna/cds.fna -a GCA_018971005.1_ASM1897100v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 13:54:12,991] [INFO] Task succeeded: Prodigal
[2023-06-19 13:54:12,992] [INFO] Task started: HMMsearch
[2023-06-19 13:54:12,992] [INFO] Running command: hmmsearch --tblout GCA_018971005.1_ASM1897100v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5442acf4-f3b8-4bcc-974a-dac211211e83/dqc_reference/reference_markers.hmm GCA_018971005.1_ASM1897100v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 13:54:13,200] [INFO] Task succeeded: HMMsearch
[2023-06-19 13:54:13,202] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg9ca9eb18-a022-480f-ba54-732d8c70388c/GCA_018971005.1_ASM1897100v1_genomic.fna.gz]
[2023-06-19 13:54:13,222] [INFO] Query marker FASTA was written to GCA_018971005.1_ASM1897100v1_genomic.fna/markers.fasta
[2023-06-19 13:54:13,223] [INFO] Task started: Blastn
[2023-06-19 13:54:13,223] [INFO] Running command: blastn -query GCA_018971005.1_ASM1897100v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5442acf4-f3b8-4bcc-974a-dac211211e83/dqc_reference/reference_markers.fasta -out GCA_018971005.1_ASM1897100v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 13:54:13,822] [INFO] Task succeeded: Blastn
[2023-06-19 13:54:13,825] [INFO] Selected 15 target genomes.
[2023-06-19 13:54:13,826] [INFO] Target genome list was writen to GCA_018971005.1_ASM1897100v1_genomic.fna/target_genomes.txt
[2023-06-19 13:54:13,831] [INFO] Task started: fastANI
[2023-06-19 13:54:13,831] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ca9eb18-a022-480f-ba54-732d8c70388c/GCA_018971005.1_ASM1897100v1_genomic.fna.gz --refList GCA_018971005.1_ASM1897100v1_genomic.fna/target_genomes.txt --output GCA_018971005.1_ASM1897100v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 13:54:24,013] [INFO] Task succeeded: fastANI
[2023-06-19 13:54:24,013] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5442acf4-f3b8-4bcc-974a-dac211211e83/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 13:54:24,013] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5442acf4-f3b8-4bcc-974a-dac211211e83/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 13:54:24,015] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 13:54:24,015] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 13:54:24,015] [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
--------------------------------------------------------------------------------
[2023-06-19 13:54:24,017] [INFO] DFAST Taxonomy check result was written to GCA_018971005.1_ASM1897100v1_genomic.fna/tc_result.tsv
[2023-06-19 13:54:24,017] [INFO] ===== Taxonomy check completed =====
[2023-06-19 13:54:24,017] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 13:54:24,017] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5442acf4-f3b8-4bcc-974a-dac211211e83/dqc_reference/checkm_data
[2023-06-19 13:54:24,020] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 13:54:24,033] [INFO] Task started: CheckM
[2023-06-19 13:54:24,033] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018971005.1_ASM1897100v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018971005.1_ASM1897100v1_genomic.fna/checkm_input GCA_018971005.1_ASM1897100v1_genomic.fna/checkm_result
[2023-06-19 13:54:40,597] [INFO] Task succeeded: CheckM
[2023-06-19 13:54:40,599] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 13:54:40,622] [INFO] ===== Completeness check finished =====
[2023-06-19 13:54:40,622] [INFO] ===== Start GTDB Search =====
[2023-06-19 13:54:40,623] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018971005.1_ASM1897100v1_genomic.fna/markers.fasta)
[2023-06-19 13:54:40,623] [INFO] Task started: Blastn
[2023-06-19 13:54:40,623] [INFO] Running command: blastn -query GCA_018971005.1_ASM1897100v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5442acf4-f3b8-4bcc-974a-dac211211e83/dqc_reference/reference_markers_gtdb.fasta -out GCA_018971005.1_ASM1897100v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 13:54:41,489] [INFO] Task succeeded: Blastn
[2023-06-19 13:54:41,493] [INFO] Selected 11 target genomes.
[2023-06-19 13:54:41,493] [INFO] Target genome list was writen to GCA_018971005.1_ASM1897100v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 13:54:41,499] [INFO] Task started: fastANI
[2023-06-19 13:54:41,500] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ca9eb18-a022-480f-ba54-732d8c70388c/GCA_018971005.1_ASM1897100v1_genomic.fna.gz --refList GCA_018971005.1_ASM1897100v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018971005.1_ASM1897100v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 13:54:44,642] [INFO] Task succeeded: fastANI
[2023-06-19 13:54:44,656] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 13:54:44,656] [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_009919005.1	s__Limnocylindrus sp009919005	97.7958	226	280	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__Limnocylindraceae;g__Limnocylindrus	95.0	97.95	97.95	0.81	0.81	2	conclusive
GCA_003670455.1	s__Limnocylindrus sp003670455	81.2439	124	280	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__Limnocylindraceae;g__Limnocylindrus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903820655.1	s__Limnocylindrus sp903820655	80.9554	105	280	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__Limnocylindraceae;g__Limnocylindrus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016463555.1	s__Limnocylindrus sp016463555	80.597	128	280	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__Limnocylindraceae;g__Limnocylindrus	95.0	98.54	98.47	0.78	0.78	3	-
GCA_009692905.1	s__Limnocylindrus sp009692905	80.5817	114	280	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__Limnocylindraceae;g__Limnocylindrus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009925905.1	s__Limnocylindrus frankliniae	80.2241	141	280	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__Limnocylindraceae;g__Limnocylindrus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009919365.1	s__Limnocylindrus sp009919365	79.4265	116	280	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__Limnocylindraceae;g__Limnocylindrus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003670475.1	s__Limnocylindrus sp003670475	77.8766	68	280	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__Limnocylindraceae;g__Limnocylindrus	95.0	98.28	98.28	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2023-06-19 13:54:44,658] [INFO] GTDB search result was written to GCA_018971005.1_ASM1897100v1_genomic.fna/result_gtdb.tsv
[2023-06-19 13:54:44,659] [INFO] ===== GTDB Search completed =====
[2023-06-19 13:54:44,661] [INFO] DFAST_QC result json was written to GCA_018971005.1_ASM1897100v1_genomic.fna/dqc_result.json
[2023-06-19 13:54:44,661] [INFO] DFAST_QC completed!
[2023-06-19 13:54:44,661] [INFO] Total running time: 0h0m36s