[2024-01-24 15:17:49,906] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:17:49,908] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:17:49,908] [INFO] DQC Reference Directory: /var/lib/cwl/stgbb46c713-2c12-49db-aecc-271537d4b6fb/dqc_reference
[2024-01-24 15:17:51,533] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:17:51,534] [INFO] Task started: Prodigal
[2024-01-24 15:17:51,535] [INFO] Running command: gunzip -c /var/lib/cwl/stg4aa0bc73-2177-46b4-b985-42c25451da1e/GCF_003966975.1_ASM396697v1_genomic.fna.gz | prodigal -d GCF_003966975.1_ASM396697v1_genomic.fna/cds.fna -a GCF_003966975.1_ASM396697v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:01,791] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:01,791] [INFO] Task started: HMMsearch
[2024-01-24 15:18:01,791] [INFO] Running command: hmmsearch --tblout GCF_003966975.1_ASM396697v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbb46c713-2c12-49db-aecc-271537d4b6fb/dqc_reference/reference_markers.hmm GCF_003966975.1_ASM396697v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:02,076] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:02,079] [INFO] Found 6/6 markers.
[2024-01-24 15:18:02,112] [INFO] Query marker FASTA was written to GCF_003966975.1_ASM396697v1_genomic.fna/markers.fasta
[2024-01-24 15:18:02,113] [INFO] Task started: Blastn
[2024-01-24 15:18:02,113] [INFO] Running command: blastn -query GCF_003966975.1_ASM396697v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb46c713-2c12-49db-aecc-271537d4b6fb/dqc_reference/reference_markers.fasta -out GCF_003966975.1_ASM396697v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:02,722] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:02,727] [INFO] Selected 16 target genomes.
[2024-01-24 15:18:02,727] [INFO] Target genome list was writen to GCF_003966975.1_ASM396697v1_genomic.fna/target_genomes.txt
[2024-01-24 15:18:02,738] [INFO] Task started: fastANI
[2024-01-24 15:18:02,738] [INFO] Running command: fastANI --query /var/lib/cwl/stg4aa0bc73-2177-46b4-b985-42c25451da1e/GCF_003966975.1_ASM396697v1_genomic.fna.gz --refList GCF_003966975.1_ASM396697v1_genomic.fna/target_genomes.txt --output GCF_003966975.1_ASM396697v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:18:12,617] [INFO] Task succeeded: fastANI
[2024-01-24 15:18:12,618] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbb46c713-2c12-49db-aecc-271537d4b6fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:18:12,619] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbb46c713-2c12-49db-aecc-271537d4b6fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:18:12,628] [INFO] Found 5 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:18:12,628] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:18:12,629] [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
Pelolinea submarina	strain=MO-CFX1	GCA_003966975.1	913107	913107	type	True	100.0	1173	1173	95	conclusive
Pelolinea submarina	strain=DSM 23923	GCA_003385075.1	913107	913107	type	True	99.9977	1166	1173	95	conclusive
Levilinea saccharolytica	strain=KIBI-1	GCA_001050255.2	229921	229921	type	True	76.8079	67	1173	95	below_threshold
Levilinea saccharolytica	strain=KIBI-1	GCA_001306035.1	229921	229921	type	True	76.7381	61	1173	95	below_threshold
Ornatilinea apprima	strain=P3M-1	GCA_001306115.1	1134406	1134406	type	True	76.3842	57	1173	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:18:12,631] [INFO] DFAST Taxonomy check result was written to GCF_003966975.1_ASM396697v1_genomic.fna/tc_result.tsv
[2024-01-24 15:18:12,639] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:18:12,639] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:18:12,640] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbb46c713-2c12-49db-aecc-271537d4b6fb/dqc_reference/checkm_data
[2024-01-24 15:18:12,641] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:18:12,684] [INFO] Task started: CheckM
[2024-01-24 15:18:12,684] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003966975.1_ASM396697v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003966975.1_ASM396697v1_genomic.fna/checkm_input GCF_003966975.1_ASM396697v1_genomic.fna/checkm_result
[2024-01-24 15:18:47,703] [INFO] Task succeeded: CheckM
[2024-01-24 15:18:47,705] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:18:47,730] [INFO] ===== Completeness check finished =====
[2024-01-24 15:18:47,731] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:18:47,731] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003966975.1_ASM396697v1_genomic.fna/markers.fasta)
[2024-01-24 15:18:47,732] [INFO] Task started: Blastn
[2024-01-24 15:18:47,732] [INFO] Running command: blastn -query GCF_003966975.1_ASM396697v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb46c713-2c12-49db-aecc-271537d4b6fb/dqc_reference/reference_markers_gtdb.fasta -out GCF_003966975.1_ASM396697v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:48,631] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:48,636] [INFO] Selected 18 target genomes.
[2024-01-24 15:18:48,636] [INFO] Target genome list was writen to GCF_003966975.1_ASM396697v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:18:48,672] [INFO] Task started: fastANI
[2024-01-24 15:18:48,672] [INFO] Running command: fastANI --query /var/lib/cwl/stg4aa0bc73-2177-46b4-b985-42c25451da1e/GCF_003966975.1_ASM396697v1_genomic.fna.gz --refList GCF_003966975.1_ASM396697v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003966975.1_ASM396697v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:18:58,332] [INFO] Task succeeded: fastANI
[2024-01-24 15:18:58,341] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:18:58,342] [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_003966975.1	s__Pelolinea submarina	100.0	1173	1173	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__Pelolinea	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCA_002412595.1	s__Pelolinea sp002412595	81.4524	629	1173	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__Pelolinea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013178095.1	s__Pelolinea sp013178095	78.0647	356	1173	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__Pelolinea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001306035.1	s__Levilinea saccharolytica	76.7381	61	1173	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__Levilinea	95.0	99.90	99.90	0.95	0.95	2	-
GCF_001306115.1	s__Ornatilinea apprima	76.3842	57	1173	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__Anaerolineaceae;g__Ornatilinea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:18:58,344] [INFO] GTDB search result was written to GCF_003966975.1_ASM396697v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:18:58,344] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:18:58,370] [INFO] DFAST_QC result json was written to GCF_003966975.1_ASM396697v1_genomic.fna/dqc_result.json
[2024-01-24 15:18:58,370] [INFO] DFAST_QC completed!
[2024-01-24 15:18:58,370] [INFO] Total running time: 0h1m8s