[2023-06-28 18:27:09,873] [INFO] DFAST_QC pipeline started.
[2023-06-28 18:27:09,875] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 18:27:09,875] [INFO] DQC Reference Directory: /var/lib/cwl/stgbd7cb9ee-7c7f-4259-baa1-b36dc5091f96/dqc_reference
[2023-06-28 18:27:11,486] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 18:27:11,498] [INFO] Task started: Prodigal
[2023-06-28 18:27:11,498] [INFO] Running command: gunzip -c /var/lib/cwl/stg70dfc7c1-0b0e-43ce-8833-eaf1d8047476/GCA_015492825.1_ASM1549282v1_genomic.fna.gz | prodigal -d GCA_015492825.1_ASM1549282v1_genomic.fna/cds.fna -a GCA_015492825.1_ASM1549282v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 18:27:21,626] [INFO] Task succeeded: Prodigal
[2023-06-28 18:27:21,627] [INFO] Task started: HMMsearch
[2023-06-28 18:27:21,627] [INFO] Running command: hmmsearch --tblout GCA_015492825.1_ASM1549282v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbd7cb9ee-7c7f-4259-baa1-b36dc5091f96/dqc_reference/reference_markers.hmm GCA_015492825.1_ASM1549282v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 18:27:21,899] [INFO] Task succeeded: HMMsearch
[2023-06-28 18:27:21,900] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg70dfc7c1-0b0e-43ce-8833-eaf1d8047476/GCA_015492825.1_ASM1549282v1_genomic.fna.gz]
[2023-06-28 18:27:21,934] [INFO] Query marker FASTA was written to GCA_015492825.1_ASM1549282v1_genomic.fna/markers.fasta
[2023-06-28 18:27:21,935] [INFO] Task started: Blastn
[2023-06-28 18:27:21,935] [INFO] Running command: blastn -query GCA_015492825.1_ASM1549282v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd7cb9ee-7c7f-4259-baa1-b36dc5091f96/dqc_reference/reference_markers.fasta -out GCA_015492825.1_ASM1549282v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:27:22,639] [INFO] Task succeeded: Blastn
[2023-06-28 18:27:22,643] [INFO] Selected 25 target genomes.
[2023-06-28 18:27:22,644] [INFO] Target genome list was writen to GCA_015492825.1_ASM1549282v1_genomic.fna/target_genomes.txt
[2023-06-28 18:27:22,647] [INFO] Task started: fastANI
[2023-06-28 18:27:22,648] [INFO] Running command: fastANI --query /var/lib/cwl/stg70dfc7c1-0b0e-43ce-8833-eaf1d8047476/GCA_015492825.1_ASM1549282v1_genomic.fna.gz --refList GCA_015492825.1_ASM1549282v1_genomic.fna/target_genomes.txt --output GCA_015492825.1_ASM1549282v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 18:27:38,020] [INFO] Task succeeded: fastANI
[2023-06-28 18:27:38,021] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbd7cb9ee-7c7f-4259-baa1-b36dc5091f96/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 18:27:38,021] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbd7cb9ee-7c7f-4259-baa1-b36dc5091f96/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 18:27:38,029] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 18:27:38,029] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 18:27:38,030] [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
Ardenticatena maritima	strain=110S	GCA_001293545.1	872965	872965	type	True	76.5626	110	971	95	below_threshold
Ardenticatena maritima	strain=110S	GCA_001306175.1	872965	872965	type	True	76.5154	115	971	95	below_threshold
Litorilinea aerophila	strain=ATCC BAA-2444	GCA_006569185.2	1204385	1204385	type	True	76.2988	87	971	95	below_threshold
Thermoflexus hugenholtzii	strain=JAD2	GCA_900187885.1	1495650	1495650	type	True	75.8256	50	971	95	below_threshold
Stigmatella erecta	strain=DSM 16858	GCA_900111745.1	83460	83460	type	True	75.0652	56	971	95	below_threshold
Azohydromonas aeria	strain=CFCC 13393	GCA_009760915.1	2590212	2590212	type	True	74.7975	51	971	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 18:27:38,032] [INFO] DFAST Taxonomy check result was written to GCA_015492825.1_ASM1549282v1_genomic.fna/tc_result.tsv
[2023-06-28 18:27:38,033] [INFO] ===== Taxonomy check completed =====
[2023-06-28 18:27:38,033] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 18:27:38,034] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbd7cb9ee-7c7f-4259-baa1-b36dc5091f96/dqc_reference/checkm_data
[2023-06-28 18:27:38,035] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 18:27:38,076] [INFO] Task started: CheckM
[2023-06-28 18:27:38,076] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_015492825.1_ASM1549282v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_015492825.1_ASM1549282v1_genomic.fna/checkm_input GCA_015492825.1_ASM1549282v1_genomic.fna/checkm_result
[2023-06-28 18:28:11,155] [INFO] Task succeeded: CheckM
[2023-06-28 18:28:11,156] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.46%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 18:28:11,180] [INFO] ===== Completeness check finished =====
[2023-06-28 18:28:11,180] [INFO] ===== Start GTDB Search =====
[2023-06-28 18:28:11,181] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_015492825.1_ASM1549282v1_genomic.fna/markers.fasta)
[2023-06-28 18:28:11,181] [INFO] Task started: Blastn
[2023-06-28 18:28:11,181] [INFO] Running command: blastn -query GCA_015492825.1_ASM1549282v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd7cb9ee-7c7f-4259-baa1-b36dc5091f96/dqc_reference/reference_markers_gtdb.fasta -out GCA_015492825.1_ASM1549282v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 18:28:12,438] [INFO] Task succeeded: Blastn
[2023-06-28 18:28:12,443] [INFO] Selected 19 target genomes.
[2023-06-28 18:28:12,443] [INFO] Target genome list was writen to GCA_015492825.1_ASM1549282v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 18:28:12,455] [INFO] Task started: fastANI
[2023-06-28 18:28:12,455] [INFO] Running command: fastANI --query /var/lib/cwl/stg70dfc7c1-0b0e-43ce-8833-eaf1d8047476/GCA_015492825.1_ASM1549282v1_genomic.fna.gz --refList GCA_015492825.1_ASM1549282v1_genomic.fna/target_genomes_gtdb.txt --output GCA_015492825.1_ASM1549282v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 18:28:24,474] [INFO] Task succeeded: fastANI
[2023-06-28 18:28:24,494] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 18:28:24,495] [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_015491235.1	s__WFWG01 sp015491235	98.9481	817	971	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Ardenticatenales;f__Ardenticatenaceae;g__WFWG01	95.0	99.02	98.95	0.84	0.84	3	conclusive
GCA_015487975.1	s__Ardenticatena sp015487975	77.6936	68	971	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Ardenticatenales;f__Ardenticatenaceae;g__Ardenticatena	95.0	99.35	99.35	0.98	0.98	2	-
GCA_015494005.1	s__S144-5 sp015494005	76.7251	86	971	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__S144-5	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001306175.1	s__Ardenticatena maritima	76.5154	115	971	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Ardenticatenales;f__Ardenticatenaceae;g__Ardenticatena	95.0	98.28	96.57	0.97	0.94	3	-
GCF_006569185.1	s__Litorilinea aerophila	76.3144	85	971	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__Litorilinea	95.0	99.85	99.85	0.99	0.99	2	-
GCA_002068935.1	s__MWBF01 sp002068935	75.7134	50	971	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__CG2-30-64-16;f__CG2-30-64-16;g__MWBF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011334325.1	s__DTPP01 sp011334325	75.6635	56	971	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__DTPP01;f__DTPP01;g__DTPP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014874485.1	s__DTLA01 sp014874485	75.6411	55	971	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__DTLA01;f__DTLA01;g__DTLA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011047455.1	s__HRBIN24 sp011047455	75.6001	60	971	d__Bacteria;p__Chloroflexota;c__Dehalococcoidia;o__SM23-28-2;f__HRbin24;g__HRBIN24	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014879765.1	s__JAAEKA01 sp014879765	75.3784	58	971	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__JAAEKA01;f__JAAEKA01;g__JAAEKA01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 18:28:24,498] [INFO] GTDB search result was written to GCA_015492825.1_ASM1549282v1_genomic.fna/result_gtdb.tsv
[2023-06-28 18:28:24,499] [INFO] ===== GTDB Search completed =====
[2023-06-28 18:28:24,502] [INFO] DFAST_QC result json was written to GCA_015492825.1_ASM1549282v1_genomic.fna/dqc_result.json
[2023-06-28 18:28:24,503] [INFO] DFAST_QC completed!
[2023-06-28 18:28:24,503] [INFO] Total running time: 0h1m15s