[2024-01-24 15:18:38,982] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:38,984] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:38,984] [INFO] DQC Reference Directory: /var/lib/cwl/stg137979c1-ad4b-4a5e-b97d-5301e8dea4b5/dqc_reference
[2024-01-24 15:18:40,249] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:40,250] [INFO] Task started: Prodigal
[2024-01-24 15:18:40,250] [INFO] Running command: gunzip -c /var/lib/cwl/stgd7718ed5-b28c-4433-8b29-659479db2627/GCF_001050215.2_ASM105021v2_genomic.fna.gz | prodigal -d GCF_001050215.2_ASM105021v2_genomic.fna/cds.fna -a GCF_001050215.2_ASM105021v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:51,936] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:51,936] [INFO] Task started: HMMsearch
[2024-01-24 15:18:51,936] [INFO] Running command: hmmsearch --tblout GCF_001050215.2_ASM105021v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg137979c1-ad4b-4a5e-b97d-5301e8dea4b5/dqc_reference/reference_markers.hmm GCF_001050215.2_ASM105021v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:52,276] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:52,277] [INFO] Found 6/6 markers.
[2024-01-24 15:18:52,317] [INFO] Query marker FASTA was written to GCF_001050215.2_ASM105021v2_genomic.fna/markers.fasta
[2024-01-24 15:18:52,318] [INFO] Task started: Blastn
[2024-01-24 15:18:52,318] [INFO] Running command: blastn -query GCF_001050215.2_ASM105021v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg137979c1-ad4b-4a5e-b97d-5301e8dea4b5/dqc_reference/reference_markers.fasta -out GCF_001050215.2_ASM105021v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:52,902] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:52,906] [INFO] Selected 20 target genomes.
[2024-01-24 15:18:52,906] [INFO] Target genome list was writen to GCF_001050215.2_ASM105021v2_genomic.fna/target_genomes.txt
[2024-01-24 15:18:52,913] [INFO] Task started: fastANI
[2024-01-24 15:18:52,914] [INFO] Running command: fastANI --query /var/lib/cwl/stgd7718ed5-b28c-4433-8b29-659479db2627/GCF_001050215.2_ASM105021v2_genomic.fna.gz --refList GCF_001050215.2_ASM105021v2_genomic.fna/target_genomes.txt --output GCF_001050215.2_ASM105021v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:19:08,456] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:08,457] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg137979c1-ad4b-4a5e-b97d-5301e8dea4b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:19:08,457] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg137979c1-ad4b-4a5e-b97d-5301e8dea4b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:19:08,464] [INFO] Found 5 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:19:08,464] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:19:08,464] [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
Bellilinea caldifistulae	strain=GOMI-1	GCA_001050215.2	360411	360411	type	True	99.9999	1231	1232	95	conclusive
Bellilinea caldifistulae	strain=GOMI-1	GCA_001306055.1	360411	360411	type	True	99.9614	1200	1232	95	conclusive
Thermanaerothrix daxensis	strain=GNS-1	GCA_001306145.1	869279	869279	type	True	76.4842	80	1232	95	below_threshold
Longilinea arvoryzae	strain=KOME-1	GCA_001050235.2	360412	360412	type	True	76.1733	72	1232	95	below_threshold
Ornatilinea apprima	strain=P3M-1	GCA_001306115.1	1134406	1134406	type	True	75.9623	68	1232	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:19:08,466] [INFO] DFAST Taxonomy check result was written to GCF_001050215.2_ASM105021v2_genomic.fna/tc_result.tsv
[2024-01-24 15:19:08,466] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:19:08,467] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:19:08,467] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg137979c1-ad4b-4a5e-b97d-5301e8dea4b5/dqc_reference/checkm_data
[2024-01-24 15:19:08,468] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:19:08,507] [INFO] Task started: CheckM
[2024-01-24 15:19:08,508] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001050215.2_ASM105021v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001050215.2_ASM105021v2_genomic.fna/checkm_input GCF_001050215.2_ASM105021v2_genomic.fna/checkm_result
[2024-01-24 15:19:45,777] [INFO] Task succeeded: CheckM
[2024-01-24 15:19:45,778] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:19:45,799] [INFO] ===== Completeness check finished =====
[2024-01-24 15:19:45,800] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:19:45,800] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001050215.2_ASM105021v2_genomic.fna/markers.fasta)
[2024-01-24 15:19:45,801] [INFO] Task started: Blastn
[2024-01-24 15:19:45,801] [INFO] Running command: blastn -query GCF_001050215.2_ASM105021v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg137979c1-ad4b-4a5e-b97d-5301e8dea4b5/dqc_reference/reference_markers_gtdb.fasta -out GCF_001050215.2_ASM105021v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:46,607] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:46,611] [INFO] Selected 23 target genomes.
[2024-01-24 15:19:46,611] [INFO] Target genome list was writen to GCF_001050215.2_ASM105021v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:19:46,630] [INFO] Task started: fastANI
[2024-01-24 15:19:46,630] [INFO] Running command: fastANI --query /var/lib/cwl/stgd7718ed5-b28c-4433-8b29-659479db2627/GCF_001050215.2_ASM105021v2_genomic.fna.gz --refList GCF_001050215.2_ASM105021v2_genomic.fna/target_genomes_gtdb.txt --output GCF_001050215.2_ASM105021v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:19:59,537] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:59,552] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:19:59,552] [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
GCF_001306055.1	s__Bellilinea caldifistulae	99.9614	1200	1232	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__Bellilinea	95.0	99.98	99.98	1.00	1.00	2	conclusive
GCA_003448875.1	s__Bellilinea sp003448875	81.0389	426	1232	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__Bellilinea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001796355.1	s__Bellilinea sp001796355	76.5045	89	1232	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__Bellilinea	95.0	99.55	99.40	0.87	0.85	3	-
GCF_001306145.1	s__Thermanaerothrix daxensis	76.4842	80	1232	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__Thermanaerothrix	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001050235.1	s__Longilinea arvoryzae	76.223	70	1232	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__Longilinea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002385985.1	s__UBA3924 sp002385985	76.1408	58	1232	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__UBA3924	95.0	99.86	99.86	0.92	0.92	2	-
GCF_001306115.1	s__Ornatilinea apprima	75.7847	67	1232	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__Ornatilinea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012798515.1	s__JAAZNB01 sp012798515	75.6831	60	1232	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__JAAZNB01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:19:59,554] [INFO] GTDB search result was written to GCF_001050215.2_ASM105021v2_genomic.fna/result_gtdb.tsv
[2024-01-24 15:19:59,555] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:19:59,557] [INFO] DFAST_QC result json was written to GCF_001050215.2_ASM105021v2_genomic.fna/dqc_result.json
[2024-01-24 15:19:59,558] [INFO] DFAST_QC completed!
[2024-01-24 15:19:59,558] [INFO] Total running time: 0h1m21s