[2023-03-15 16:02:07,986] [INFO] DFAST_QC pipeline started.
[2023-03-15 16:02:07,986] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 16:02:07,986] [INFO] DQC Reference Directory: /var/lib/cwl/stgcf22cadf-80c6-4479-b74c-9cec6ebf7388/dqc_reference
[2023-03-15 16:02:09,101] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 16:02:09,101] [INFO] Task started: Prodigal
[2023-03-15 16:02:09,101] [INFO] Running command: cat /var/lib/cwl/stg9a97fb96-50bc-4d20-abe6-b16ae90cbc11/OceanDNA-b34918.fa | prodigal -d OceanDNA-b34918/cds.fna -a OceanDNA-b34918/protein.faa -g 11 -q > /dev/null
[2023-03-15 16:02:38,123] [INFO] Task succeeded: Prodigal
[2023-03-15 16:02:38,123] [INFO] Task started: HMMsearch
[2023-03-15 16:02:38,123] [INFO] Running command: hmmsearch --tblout OceanDNA-b34918/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcf22cadf-80c6-4479-b74c-9cec6ebf7388/dqc_reference/reference_markers.hmm OceanDNA-b34918/protein.faa > /dev/null
[2023-03-15 16:02:38,373] [INFO] Task succeeded: HMMsearch
[2023-03-15 16:02:38,373] [INFO] Found 6/6 markers.
[2023-03-15 16:02:38,407] [INFO] Query marker FASTA was written to OceanDNA-b34918/markers.fasta
[2023-03-15 16:02:38,408] [INFO] Task started: Blastn
[2023-03-15 16:02:38,409] [INFO] Running command: blastn -query OceanDNA-b34918/markers.fasta -db /var/lib/cwl/stgcf22cadf-80c6-4479-b74c-9cec6ebf7388/dqc_reference/reference_markers.fasta -out OceanDNA-b34918/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:02:39,070] [INFO] Task succeeded: Blastn
[2023-03-15 16:02:39,071] [INFO] Selected 22 target genomes.
[2023-03-15 16:02:39,071] [INFO] Target genome list was writen to OceanDNA-b34918/target_genomes.txt
[2023-03-15 16:02:39,087] [INFO] Task started: fastANI
[2023-03-15 16:02:39,087] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a97fb96-50bc-4d20-abe6-b16ae90cbc11/OceanDNA-b34918.fa --refList OceanDNA-b34918/target_genomes.txt --output OceanDNA-b34918/fastani_result.tsv --threads 1
[2023-03-15 16:02:55,155] [INFO] Task succeeded: fastANI
[2023-03-15 16:02:55,156] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcf22cadf-80c6-4479-b74c-9cec6ebf7388/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 16:02:55,156] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcf22cadf-80c6-4479-b74c-9cec6ebf7388/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 16:02:55,164] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 16:02:55,164] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 16:02:55,164] [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
Paraglaciecola mesophila	strain=KMM 241	GCA_000315015.1	197222	197222	type	True	83.1518	992	1711	95	below_threshold
Paraglaciecola polaris	strain=LMG 21857	GCA_000315055.1	222814	222814	type	True	80.3478	691	1711	95	below_threshold
Alteromonas lipotrueae	strain=MD_652	GCA_019249215.1	2803814	2803814	type	True	78.9496	111	1711	95	below_threshold
Paraglaciecola aquimarina	strain=GGW-M5	GCA_021532655.1	1235557	1235557	type	True	77.9118	151	1711	95	below_threshold
Paraglaciecola marina	strain=D3211	GCA_004360155.1	2500157	2500157	type	True	77.886	137	1711	95	below_threshold
Alteromonas sediminis	strain=U0105	GCA_003820355.1	2259342	2259342	type	True	77.7951	54	1711	95	below_threshold
Paraglaciecola hydrolytica	strain=S66	GCA_001565895.1	1799789	1799789	type	True	77.5862	161	1711	95	below_threshold
Paraglaciecola arctica	strain=BSs20135	GCA_000314995.1	1128911	1128911	type	True	77.4753	160	1711	95	below_threshold
Alteromonas naphthalenivorans	strain=SN2	GCA_000213655.1	715451	715451	type	True	77.1954	119	1711	95	below_threshold
Neptunicella marina	strain=S27-2	GCA_014270035.1	2125989	2125989	type	True	76.9854	82	1711	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 16:02:55,164] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34918/tc_result.tsv
[2023-03-15 16:02:55,164] [INFO] ===== Taxonomy check completed =====
[2023-03-15 16:02:55,165] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 16:02:55,165] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcf22cadf-80c6-4479-b74c-9cec6ebf7388/dqc_reference/checkm_data
[2023-03-15 16:02:55,165] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 16:02:55,246] [INFO] Task started: CheckM
[2023-03-15 16:02:55,246] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34918/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34918/checkm_input OceanDNA-b34918/checkm_result
[2023-03-15 16:04:05,871] [INFO] Task succeeded: CheckM
[2023-03-15 16:04:05,871] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 16:04:05,874] [INFO] ===== Completeness check finished =====
[2023-03-15 16:04:05,875] [INFO] ===== Start GTDB Search =====
[2023-03-15 16:04:05,875] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34918/markers.fasta)
[2023-03-15 16:04:05,876] [INFO] Task started: Blastn
[2023-03-15 16:04:05,876] [INFO] Running command: blastn -query OceanDNA-b34918/markers.fasta -db /var/lib/cwl/stgcf22cadf-80c6-4479-b74c-9cec6ebf7388/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34918/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 16:04:06,933] [INFO] Task succeeded: Blastn
[2023-03-15 16:04:06,935] [INFO] Selected 8 target genomes.
[2023-03-15 16:04:06,935] [INFO] Target genome list was writen to OceanDNA-b34918/target_genomes_gtdb.txt
[2023-03-15 16:04:06,946] [INFO] Task started: fastANI
[2023-03-15 16:04:06,946] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a97fb96-50bc-4d20-abe6-b16ae90cbc11/OceanDNA-b34918.fa --refList OceanDNA-b34918/target_genomes_gtdb.txt --output OceanDNA-b34918/fastani_result_gtdb.tsv --threads 1
[2023-03-15 16:04:16,022] [INFO] Task succeeded: fastANI
[2023-03-15 16:04:16,028] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 16:04:16,028] [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_000314955.1	s__Paraglaciecola chathamensis	98.4883	1521	1711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	98.24	97.58	0.90	0.88	8	conclusive
GCF_009906955.1	s__Paraglaciecola mesophila_A	89.9112	1386	1711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000315015.1	s__Paraglaciecola mesophila	83.1295	994	1711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	98.29	98.05	0.87	0.80	4	-
GCF_000014225.1	s__Paraglaciecola atlantica_A	81.6729	967	1711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000315055.1	s__Paraglaciecola polaris	80.3478	691	1711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009796745.1	s__Paraglaciecola sp009796745	80.1122	626	1711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011378905.1	s__Paraglaciecola sp011378905	79.8682	662	1711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Paraglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007197995.1	s__Aliiglaciecola sp007197995	77.5339	93	1711	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Aliiglaciecola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 16:04:16,029] [INFO] GTDB search result was written to OceanDNA-b34918/result_gtdb.tsv
[2023-03-15 16:04:16,029] [INFO] ===== GTDB Search completed =====
[2023-03-15 16:04:16,030] [INFO] DFAST_QC result json was written to OceanDNA-b34918/dqc_result.json
[2023-03-15 16:04:16,030] [INFO] DFAST_QC completed!
[2023-03-15 16:04:16,030] [INFO] Total running time: 0h2m8s