[2023-06-17 04:57:03,335] [INFO] DFAST_QC pipeline started.
[2023-06-17 04:57:03,337] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 04:57:03,337] [INFO] DQC Reference Directory: /var/lib/cwl/stgac151add-6b5f-4700-8acf-5224e3de4735/dqc_reference
[2023-06-17 04:57:05,165] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 04:57:05,167] [INFO] Task started: Prodigal
[2023-06-17 04:57:05,167] [INFO] Running command: gunzip -c /var/lib/cwl/stgbe4ce1c4-af1a-484c-978d-4bfb4919dfb2/GCA_013335525.1_ASM1333552v1_genomic.fna.gz | prodigal -d GCA_013335525.1_ASM1333552v1_genomic.fna/cds.fna -a GCA_013335525.1_ASM1333552v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 04:57:14,452] [INFO] Task succeeded: Prodigal
[2023-06-17 04:57:14,453] [INFO] Task started: HMMsearch
[2023-06-17 04:57:14,453] [INFO] Running command: hmmsearch --tblout GCA_013335525.1_ASM1333552v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgac151add-6b5f-4700-8acf-5224e3de4735/dqc_reference/reference_markers.hmm GCA_013335525.1_ASM1333552v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 04:57:14,677] [INFO] Task succeeded: HMMsearch
[2023-06-17 04:57:14,679] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgbe4ce1c4-af1a-484c-978d-4bfb4919dfb2/GCA_013335525.1_ASM1333552v1_genomic.fna.gz]
[2023-06-17 04:57:14,706] [INFO] Query marker FASTA was written to GCA_013335525.1_ASM1333552v1_genomic.fna/markers.fasta
[2023-06-17 04:57:14,706] [INFO] Task started: Blastn
[2023-06-17 04:57:14,706] [INFO] Running command: blastn -query GCA_013335525.1_ASM1333552v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgac151add-6b5f-4700-8acf-5224e3de4735/dqc_reference/reference_markers.fasta -out GCA_013335525.1_ASM1333552v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 04:57:15,219] [INFO] Task succeeded: Blastn
[2023-06-17 04:57:15,225] [INFO] Selected 8 target genomes.
[2023-06-17 04:57:15,225] [INFO] Target genome list was writen to GCA_013335525.1_ASM1333552v1_genomic.fna/target_genomes.txt
[2023-06-17 04:57:15,229] [INFO] Task started: fastANI
[2023-06-17 04:57:15,229] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe4ce1c4-af1a-484c-978d-4bfb4919dfb2/GCA_013335525.1_ASM1333552v1_genomic.fna.gz --refList GCA_013335525.1_ASM1333552v1_genomic.fna/target_genomes.txt --output GCA_013335525.1_ASM1333552v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 04:57:19,318] [INFO] Task succeeded: fastANI
[2023-06-17 04:57:19,319] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgac151add-6b5f-4700-8acf-5224e3de4735/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 04:57:19,319] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgac151add-6b5f-4700-8acf-5224e3de4735/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 04:57:19,330] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 04:57:19,331] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 04:57:19,331] [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
Pelodictyon phaeoclathratiforme	strain=BU-1	GCA_000020645.1	34090	34090	type	True	77.5116	59	401	95	below_threshold
Chlorobaculum limnaeum	strain=DSM 1677	GCA_001747405.1	274537	274537	type	True	77.2594	66	401	95	below_threshold
Chlorobium limicola	strain=DSM 245	GCA_000020465.1	1092	1092	type	True	77.2549	76	401	95	below_threshold
Chlorobium phaeobacteroides	strain=DSM 266	GCA_000015125.1	1096	1096	type	True	77.1338	65	401	95	below_threshold
Chlorobium ferrooxidans	strain=DSM 13031	GCA_000168715.1	84205	84205	type	True	77.0279	69	401	95	below_threshold
Chlorobaculum thiosulfatiphilum	strain=DSM 249	GCA_006265165.1	115852	115852	type	True	76.9613	71	401	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 04:57:19,334] [INFO] DFAST Taxonomy check result was written to GCA_013335525.1_ASM1333552v1_genomic.fna/tc_result.tsv
[2023-06-17 04:57:19,334] [INFO] ===== Taxonomy check completed =====
[2023-06-17 04:57:19,334] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 04:57:19,335] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgac151add-6b5f-4700-8acf-5224e3de4735/dqc_reference/checkm_data
[2023-06-17 04:57:19,337] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 04:57:19,371] [INFO] Task started: CheckM
[2023-06-17 04:57:19,372] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013335525.1_ASM1333552v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013335525.1_ASM1333552v1_genomic.fna/checkm_input GCA_013335525.1_ASM1333552v1_genomic.fna/checkm_result
[2023-06-17 04:57:51,899] [INFO] Task succeeded: CheckM
[2023-06-17 04:57:51,900] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.04%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 04:57:51,919] [INFO] ===== Completeness check finished =====
[2023-06-17 04:57:51,919] [INFO] ===== Start GTDB Search =====
[2023-06-17 04:57:51,920] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013335525.1_ASM1333552v1_genomic.fna/markers.fasta)
[2023-06-17 04:57:51,920] [INFO] Task started: Blastn
[2023-06-17 04:57:51,920] [INFO] Running command: blastn -query GCA_013335525.1_ASM1333552v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgac151add-6b5f-4700-8acf-5224e3de4735/dqc_reference/reference_markers_gtdb.fasta -out GCA_013335525.1_ASM1333552v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 04:57:52,406] [INFO] Task succeeded: Blastn
[2023-06-17 04:57:52,410] [INFO] Selected 8 target genomes.
[2023-06-17 04:57:52,410] [INFO] Target genome list was writen to GCA_013335525.1_ASM1333552v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 04:57:52,415] [INFO] Task started: fastANI
[2023-06-17 04:57:52,415] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe4ce1c4-af1a-484c-978d-4bfb4919dfb2/GCA_013335525.1_ASM1333552v1_genomic.fna.gz --refList GCA_013335525.1_ASM1333552v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013335525.1_ASM1333552v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 04:57:55,814] [INFO] Task succeeded: fastANI
[2023-06-17 04:57:55,830] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-17 04:57:55,830] [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_013335405.1	s__Chlorobium sp013335405	82.9782	315	401	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.91	99.91	0.96	0.96	2	-
GCA_013334565.1	s__Chlorobium sp013334565	81.0301	250	401	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903928225.1	s__Chlorobium sp903928225	80.5741	268	401	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.78	99.75	0.93	0.92	5	-
GCA_005862285.1	s__Chlorobium sp005862285	79.7893	182	401	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013334225.1	s__Chlorobium sp013334225	79.6839	192	401	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903820085.1	s__Chlorobium sp903820085	77.47	71	401	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.98	99.89	0.98	0.91	15	-
GCA_903824045.1	s__Chlorobium sp903824045	77.3041	80	401	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	99.97	99.92	0.98	0.96	6	-
GCA_903940125.1	s__Chlorobium sp903940125	76.9713	57	401	d__Bacteria;p__Bacteroidota;c__Chlorobia;o__Chlorobiales;f__Chlorobiaceae;g__Chlorobium	95.0	98.50	97.06	0.88	0.72	14	-
--------------------------------------------------------------------------------
[2023-06-17 04:57:55,832] [INFO] GTDB search result was written to GCA_013335525.1_ASM1333552v1_genomic.fna/result_gtdb.tsv
[2023-06-17 04:57:55,833] [INFO] ===== GTDB Search completed =====
[2023-06-17 04:57:55,838] [INFO] DFAST_QC result json was written to GCA_013335525.1_ASM1333552v1_genomic.fna/dqc_result.json
[2023-06-17 04:57:55,839] [INFO] DFAST_QC completed!
[2023-06-17 04:57:55,839] [INFO] Total running time: 0h0m53s