[2023-03-15 03:56:21,757] [INFO] DFAST_QC pipeline started.
[2023-03-15 03:56:21,757] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 03:56:21,757] [INFO] DQC Reference Directory: /var/lib/cwl/stg0ecda7e1-8037-45b1-ba2f-94778a58cbc3/dqc_reference
[2023-03-15 03:56:23,409] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 03:56:23,409] [INFO] Task started: Prodigal
[2023-03-15 03:56:23,409] [INFO] Running command: cat /var/lib/cwl/stgcfc72107-7394-4a8d-a47b-ccfa264224af/OceanDNA-b3696.fa | prodigal -d OceanDNA-b3696/cds.fna -a OceanDNA-b3696/protein.faa -g 11 -q > /dev/null
[2023-03-15 03:56:48,000] [INFO] Task succeeded: Prodigal
[2023-03-15 03:56:48,000] [INFO] Task started: HMMsearch
[2023-03-15 03:56:48,000] [INFO] Running command: hmmsearch --tblout OceanDNA-b3696/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0ecda7e1-8037-45b1-ba2f-94778a58cbc3/dqc_reference/reference_markers.hmm OceanDNA-b3696/protein.faa > /dev/null
[2023-03-15 03:56:48,262] [INFO] Task succeeded: HMMsearch
[2023-03-15 03:56:48,263] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgcfc72107-7394-4a8d-a47b-ccfa264224af/OceanDNA-b3696.fa]
[2023-03-15 03:56:48,284] [INFO] Query marker FASTA was written to OceanDNA-b3696/markers.fasta
[2023-03-15 03:56:48,285] [INFO] Task started: Blastn
[2023-03-15 03:56:48,285] [INFO] Running command: blastn -query OceanDNA-b3696/markers.fasta -db /var/lib/cwl/stg0ecda7e1-8037-45b1-ba2f-94778a58cbc3/dqc_reference/reference_markers.fasta -out OceanDNA-b3696/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:56:48,837] [INFO] Task succeeded: Blastn
[2023-03-15 03:56:48,838] [INFO] Selected 7 target genomes.
[2023-03-15 03:56:48,838] [INFO] Target genome list was writen to OceanDNA-b3696/target_genomes.txt
[2023-03-15 03:56:48,844] [INFO] Task started: fastANI
[2023-03-15 03:56:48,844] [INFO] Running command: fastANI --query /var/lib/cwl/stgcfc72107-7394-4a8d-a47b-ccfa264224af/OceanDNA-b3696.fa --refList OceanDNA-b3696/target_genomes.txt --output OceanDNA-b3696/fastani_result.tsv --threads 1
[2023-03-15 03:56:56,095] [INFO] Task succeeded: fastANI
[2023-03-15 03:56:56,095] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0ecda7e1-8037-45b1-ba2f-94778a58cbc3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 03:56:56,095] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0ecda7e1-8037-45b1-ba2f-94778a58cbc3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 03:56:56,101] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 03:56:56,101] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 03:56:56,101] [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
Neolewinella marina	strain=MKG-38	GCA_002631205.1	438751	438751	type	True	80.4612	625	983	95	below_threshold
Neolewinella marina	strain=DSM 104084	GCA_011927705.1	438751	438751	type	True	80.4482	629	983	95	below_threshold
Neolewinella litorea	strain=HSMS-39	GCA_004803465.1	2562452	2562452	type	True	79.706	531	983	95	below_threshold
Neolewinella maritima	strain=CECT 8419, type strain	GCA_923081025.1	1383882	1383882	type	True	78.5362	446	983	95	below_threshold
Neolewinella xylanilytica	strain=DSM 29526	GCA_002934605.1	1514080	1514080	type	True	78.4343	476	983	95	below_threshold
Neolewinella aquimaris	strain=DSM 105137	GCA_014197245.1	1835722	1835722	type	True	78.3153	424	983	95	below_threshold
Neolewinella lacunae	strain=KCTC 42187	GCA_014349155.1	1517758	1517758	type	True	76.9908	215	983	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 03:56:56,101] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3696/tc_result.tsv
[2023-03-15 03:56:56,102] [INFO] ===== Taxonomy check completed =====
[2023-03-15 03:56:56,102] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 03:56:56,102] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0ecda7e1-8037-45b1-ba2f-94778a58cbc3/dqc_reference/checkm_data
[2023-03-15 03:56:56,103] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 03:56:56,109] [INFO] Task started: CheckM
[2023-03-15 03:56:56,109] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3696/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3696/checkm_input OceanDNA-b3696/checkm_result
[2023-03-15 03:57:56,023] [INFO] Task succeeded: CheckM
[2023-03-15 03:57:56,024] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 55.68%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 03:57:56,029] [INFO] ===== Completeness check finished =====
[2023-03-15 03:57:56,029] [INFO] ===== Start GTDB Search =====
[2023-03-15 03:57:56,029] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3696/markers.fasta)
[2023-03-15 03:57:56,030] [INFO] Task started: Blastn
[2023-03-15 03:57:56,030] [INFO] Running command: blastn -query OceanDNA-b3696/markers.fasta -db /var/lib/cwl/stg0ecda7e1-8037-45b1-ba2f-94778a58cbc3/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3696/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 03:57:56,865] [INFO] Task succeeded: Blastn
[2023-03-15 03:57:56,867] [INFO] Selected 7 target genomes.
[2023-03-15 03:57:56,867] [INFO] Target genome list was writen to OceanDNA-b3696/target_genomes_gtdb.txt
[2023-03-15 03:57:56,875] [INFO] Task started: fastANI
[2023-03-15 03:57:56,875] [INFO] Running command: fastANI --query /var/lib/cwl/stgcfc72107-7394-4a8d-a47b-ccfa264224af/OceanDNA-b3696.fa --refList OceanDNA-b3696/target_genomes_gtdb.txt --output OceanDNA-b3696/fastani_result_gtdb.tsv --threads 1
[2023-03-15 03:58:03,334] [INFO] Task succeeded: fastANI
[2023-03-15 03:58:03,339] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 03:58:03,339] [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_003390915.1	s__Lewinella_A sp003390915	81.0737	688	983	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002631205.1	s__Lewinella_A marina	80.4611	625	983	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004803465.1	s__Lewinella_A litorea	79.716	530	983	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003390935.1	s__Lewinella_A sp003390935	78.4519	433	983	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002934605.1	s__Lewinella_A xylanilytica	78.4349	476	983	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197245.1	s__Lewinella_A aquimaris	78.3335	422	983	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014349155.1	s__Lewinella_A lacunae	76.9908	215	983	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__Lewinella_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 03:58:03,339] [INFO] GTDB search result was written to OceanDNA-b3696/result_gtdb.tsv
[2023-03-15 03:58:03,339] [INFO] ===== GTDB Search completed =====
[2023-03-15 03:58:03,341] [INFO] DFAST_QC result json was written to OceanDNA-b3696/dqc_result.json
[2023-03-15 03:58:03,341] [INFO] DFAST_QC completed!
[2023-03-15 03:58:03,341] [INFO] Total running time: 0h1m42s