[2024-01-24 13:49:55,425] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:55,426] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:55,427] [INFO] DQC Reference Directory: /var/lib/cwl/stg6233cfd3-57e4-4a0d-8342-9ec44c3ca2d2/dqc_reference
[2024-01-24 13:49:56,691] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:56,692] [INFO] Task started: Prodigal
[2024-01-24 13:49:56,692] [INFO] Running command: gunzip -c /var/lib/cwl/stgcd1f0bd7-ad4c-4c7d-8213-ca910ff7dc94/GCF_005116675.2_ASM511667v2_genomic.fna.gz | prodigal -d GCF_005116675.2_ASM511667v2_genomic.fna/cds.fna -a GCF_005116675.2_ASM511667v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:50:12,409] [INFO] Task succeeded: Prodigal
[2024-01-24 13:50:12,410] [INFO] Task started: HMMsearch
[2024-01-24 13:50:12,410] [INFO] Running command: hmmsearch --tblout GCF_005116675.2_ASM511667v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6233cfd3-57e4-4a0d-8342-9ec44c3ca2d2/dqc_reference/reference_markers.hmm GCF_005116675.2_ASM511667v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:50:12,715] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:50:12,717] [INFO] Found 6/6 markers.
[2024-01-24 13:50:12,760] [INFO] Query marker FASTA was written to GCF_005116675.2_ASM511667v2_genomic.fna/markers.fasta
[2024-01-24 13:50:12,761] [INFO] Task started: Blastn
[2024-01-24 13:50:12,761] [INFO] Running command: blastn -query GCF_005116675.2_ASM511667v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg6233cfd3-57e4-4a0d-8342-9ec44c3ca2d2/dqc_reference/reference_markers.fasta -out GCF_005116675.2_ASM511667v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:13,359] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:13,363] [INFO] Selected 21 target genomes.
[2024-01-24 13:50:13,364] [INFO] Target genome list was writen to GCF_005116675.2_ASM511667v2_genomic.fna/target_genomes.txt
[2024-01-24 13:50:13,371] [INFO] Task started: fastANI
[2024-01-24 13:50:13,372] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd1f0bd7-ad4c-4c7d-8213-ca910ff7dc94/GCF_005116675.2_ASM511667v2_genomic.fna.gz --refList GCF_005116675.2_ASM511667v2_genomic.fna/target_genomes.txt --output GCF_005116675.2_ASM511667v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:28,013] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:28,014] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6233cfd3-57e4-4a0d-8342-9ec44c3ca2d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:28,014] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6233cfd3-57e4-4a0d-8342-9ec44c3ca2d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:28,020] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:28,020] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:28,020] [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
Desulfosediminicola ganghwensis	strain=IMCC35004	GCA_005116675.2	2569540	2569540	type	True	100.0	1883	1884	95	conclusive
Desulfotalea psychrophila	strain=LSv54	GCA_000025945.1	84980	84980	type	True	79.5802	59	1884	95	below_threshold
Desulfosediminicola flagellatus	strain=IMCC35005	GCA_005116655.2	2569541	2569541	type	True	78.3128	250	1884	95	below_threshold
Desulfopila aestuarii	strain=DSM 18488	GCA_900143695.1	231440	231440	type	True	77.4282	199	1884	95	below_threshold
Desulfoprunum benzoelyticum	strain=DSM 28570	GCA_014201505.1	1506996	1506996	type	True	76.6832	56	1884	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:28,021] [INFO] DFAST Taxonomy check result was written to GCF_005116675.2_ASM511667v2_genomic.fna/tc_result.tsv
[2024-01-24 13:50:28,022] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:28,022] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:28,022] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6233cfd3-57e4-4a0d-8342-9ec44c3ca2d2/dqc_reference/checkm_data
[2024-01-24 13:50:28,023] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:28,080] [INFO] Task started: CheckM
[2024-01-24 13:50:28,081] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005116675.2_ASM511667v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005116675.2_ASM511667v2_genomic.fna/checkm_input GCF_005116675.2_ASM511667v2_genomic.fna/checkm_result
[2024-01-24 13:51:15,606] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:15,607] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:51:15,631] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:15,631] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:15,632] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005116675.2_ASM511667v2_genomic.fna/markers.fasta)
[2024-01-24 13:51:15,632] [INFO] Task started: Blastn
[2024-01-24 13:51:15,633] [INFO] Running command: blastn -query GCF_005116675.2_ASM511667v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg6233cfd3-57e4-4a0d-8342-9ec44c3ca2d2/dqc_reference/reference_markers_gtdb.fasta -out GCF_005116675.2_ASM511667v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:16,387] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:16,392] [INFO] Selected 27 target genomes.
[2024-01-24 13:51:16,392] [INFO] Target genome list was writen to GCF_005116675.2_ASM511667v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:16,504] [INFO] Task started: fastANI
[2024-01-24 13:51:16,505] [INFO] Running command: fastANI --query /var/lib/cwl/stgcd1f0bd7-ad4c-4c7d-8213-ca910ff7dc94/GCF_005116675.2_ASM511667v2_genomic.fna.gz --refList GCF_005116675.2_ASM511667v2_genomic.fna/target_genomes_gtdb.txt --output GCF_005116675.2_ASM511667v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:33,238] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:33,249] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:33,249] [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_005116675.2	s__Desulfopila sp005116675	100.0	1882	1884	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__Desulfopila	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_005116655.2	s__Desulfopila sp005116655	78.3156	250	1884	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__Desulfopila	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010646885.1	s__Desulfopila sp010646885	77.6077	151	1884	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__Desulfopila	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900143695.1	s__Desulfopila aestuarii	77.4282	199	1884	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__Desulfopila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011390165.1	s__Desulforhopalus sp011390165	76.3705	57	1884	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__Desulforhopalus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013139415.1	s__Desulforhopalus sp013139415	76.28	64	1884	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__Desulforhopalus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003249645.1	s__SZUA-575 sp003249645	76.23	69	1884	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__SZUA-575	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008933635.1	s__Desulfoprunum sp008933635	76.1891	72	1884	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfocapsaceae;g__Desulfoprunum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:51:33,251] [INFO] GTDB search result was written to GCF_005116675.2_ASM511667v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:33,251] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:33,254] [INFO] DFAST_QC result json was written to GCF_005116675.2_ASM511667v2_genomic.fna/dqc_result.json
[2024-01-24 13:51:33,254] [INFO] DFAST_QC completed!
[2024-01-24 13:51:33,254] [INFO] Total running time: 0h1m38s