[2024-01-24 11:26:54,308] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:54,310] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:54,310] [INFO] DQC Reference Directory: /var/lib/cwl/stg9b3f0b2b-f4d8-4d67-ade2-08cd1be7267d/dqc_reference
[2024-01-24 11:26:58,222] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:58,224] [INFO] Task started: Prodigal
[2024-01-24 11:26:58,224] [INFO] Running command: gunzip -c /var/lib/cwl/stg9b1b46c5-47a8-44e8-994b-1de094e494b0/GCF_016908145.1_ASM1690814v1_genomic.fna.gz | prodigal -d GCF_016908145.1_ASM1690814v1_genomic.fna/cds.fna -a GCF_016908145.1_ASM1690814v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:27:01,599] [INFO] Task succeeded: Prodigal
[2024-01-24 11:27:01,599] [INFO] Task started: HMMsearch
[2024-01-24 11:27:01,599] [INFO] Running command: hmmsearch --tblout GCF_016908145.1_ASM1690814v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9b3f0b2b-f4d8-4d67-ade2-08cd1be7267d/dqc_reference/reference_markers.hmm GCF_016908145.1_ASM1690814v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:27:01,839] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:27:01,841] [INFO] Found 6/6 markers.
[2024-01-24 11:27:01,869] [INFO] Query marker FASTA was written to GCF_016908145.1_ASM1690814v1_genomic.fna/markers.fasta
[2024-01-24 11:27:01,869] [INFO] Task started: Blastn
[2024-01-24 11:27:01,869] [INFO] Running command: blastn -query GCF_016908145.1_ASM1690814v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9b3f0b2b-f4d8-4d67-ade2-08cd1be7267d/dqc_reference/reference_markers.fasta -out GCF_016908145.1_ASM1690814v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:03,744] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:03,748] [INFO] Selected 11 target genomes.
[2024-01-24 11:27:03,748] [INFO] Target genome list was writen to GCF_016908145.1_ASM1690814v1_genomic.fna/target_genomes.txt
[2024-01-24 11:27:03,823] [INFO] Task started: fastANI
[2024-01-24 11:27:03,824] [INFO] Running command: fastANI --query /var/lib/cwl/stg9b1b46c5-47a8-44e8-994b-1de094e494b0/GCF_016908145.1_ASM1690814v1_genomic.fna.gz --refList GCF_016908145.1_ASM1690814v1_genomic.fna/target_genomes.txt --output GCF_016908145.1_ASM1690814v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:27:08,798] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:08,799] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9b3f0b2b-f4d8-4d67-ade2-08cd1be7267d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:27:08,799] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9b3f0b2b-f4d8-4d67-ade2-08cd1be7267d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:27:08,806] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:27:08,807] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:27:08,807] [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
Marinitoga litoralis	strain=DSM 21709	GCA_016908145.1	570855	570855	type	True	100.0	718	720	95	conclusive
Marinitoga lauensis	strain=LG1	GCA_004135675.1	2201189	2201189	type	True	80.5913	473	720	95	below_threshold
Marinitoga hydrogenitolerans	strain=DSM 16785	GCA_900129175.1	287990	287990	type	True	79.9749	443	720	95	below_threshold
Marinitoga piezophila	strain=KA3	GCA_000255135.1	149715	149715	type	True	78.9249	332	720	95	below_threshold
Tepiditoga spiralis	strain=sy52	GCA_014701195.1	2108365	2108365	type	True	75.771	164	720	95	below_threshold
Clostridium bornimense	strain=type strain: M2/40	GCA_000577895.1	1216932	1216932	type	True	74.7061	57	720	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:27:08,808] [INFO] DFAST Taxonomy check result was written to GCF_016908145.1_ASM1690814v1_genomic.fna/tc_result.tsv
[2024-01-24 11:27:08,809] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:27:08,809] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:27:08,809] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9b3f0b2b-f4d8-4d67-ade2-08cd1be7267d/dqc_reference/checkm_data
[2024-01-24 11:27:08,811] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:27:08,839] [INFO] Task started: CheckM
[2024-01-24 11:27:08,840] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016908145.1_ASM1690814v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016908145.1_ASM1690814v1_genomic.fna/checkm_input GCF_016908145.1_ASM1690814v1_genomic.fna/checkm_result
[2024-01-24 11:27:28,133] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:28,135] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.93%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:28,156] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:28,156] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:28,157] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016908145.1_ASM1690814v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:28,158] [INFO] Task started: Blastn
[2024-01-24 11:27:28,158] [INFO] Running command: blastn -query GCF_016908145.1_ASM1690814v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9b3f0b2b-f4d8-4d67-ade2-08cd1be7267d/dqc_reference/reference_markers_gtdb.fasta -out GCF_016908145.1_ASM1690814v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:29,007] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:29,011] [INFO] Selected 7 target genomes.
[2024-01-24 11:27:29,011] [INFO] Target genome list was writen to GCF_016908145.1_ASM1690814v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:29,019] [INFO] Task started: fastANI
[2024-01-24 11:27:29,020] [INFO] Running command: fastANI --query /var/lib/cwl/stg9b1b46c5-47a8-44e8-994b-1de094e494b0/GCF_016908145.1_ASM1690814v1_genomic.fna.gz --refList GCF_016908145.1_ASM1690814v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016908145.1_ASM1690814v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:27:33,182] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:33,195] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:27:33,195] [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_016908145.1	s__Marinitoga litoralis	100.0	718	720	d__Bacteria;p__Thermotogota;c__Thermotogae;o__Petrotogales;f__Petrotogaceae;g__Marinitoga	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_011057715.1	s__Marinitoga sp011057715	85.5657	570	720	d__Bacteria;p__Thermotogota;c__Thermotogae;o__Petrotogales;f__Petrotogaceae;g__Marinitoga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004135675.1	s__Marinitoga lauensis	80.5647	476	720	d__Bacteria;p__Thermotogota;c__Thermotogae;o__Petrotogales;f__Petrotogaceae;g__Marinitoga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129175.1	s__Marinitoga hydrogenitolerans	79.9535	444	720	d__Bacteria;p__Thermotogota;c__Thermotogae;o__Petrotogales;f__Petrotogaceae;g__Marinitoga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001021165.1	s__Marinitoga sp001021165	79.5264	404	720	d__Bacteria;p__Thermotogota;c__Thermotogae;o__Petrotogales;f__Petrotogaceae;g__Marinitoga	95.0	96.86	96.83	0.88	0.88	3	-
GCF_014701195.1	s__Tepiditoga spiralis	75.797	164	720	d__Bacteria;p__Thermotogota;c__Thermotogae;o__Petrotogales;f__Petrotogaceae;g__Tepiditoga	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:27:33,197] [INFO] GTDB search result was written to GCF_016908145.1_ASM1690814v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:27:33,198] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:27:33,202] [INFO] DFAST_QC result json was written to GCF_016908145.1_ASM1690814v1_genomic.fna/dqc_result.json
[2024-01-24 11:27:33,202] [INFO] DFAST_QC completed!
[2024-01-24 11:27:33,202] [INFO] Total running time: 0h0m39s