[2023-03-17 11:08:00,273] [INFO] DFAST_QC pipeline started.
[2023-03-17 11:08:00,277] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 11:08:00,277] [INFO] DQC Reference Directory: /var/lib/cwl/stg4601f105-adc2-4d47-8760-0d36f88bfe1c/dqc_reference
[2023-03-17 11:08:01,419] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 11:08:01,419] [INFO] Task started: Prodigal
[2023-03-17 11:08:01,420] [INFO] Running command: cat /var/lib/cwl/stg299e4f95-3f98-40ad-9b93-6ae31ba1b943/OceanDNA-b12387.fa | prodigal -d OceanDNA-b12387/cds.fna -a OceanDNA-b12387/protein.faa -g 11 -q > /dev/null
[2023-03-17 11:08:14,860] [INFO] Task succeeded: Prodigal
[2023-03-17 11:08:14,860] [INFO] Task started: HMMsearch
[2023-03-17 11:08:14,860] [INFO] Running command: hmmsearch --tblout OceanDNA-b12387/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4601f105-adc2-4d47-8760-0d36f88bfe1c/dqc_reference/reference_markers.hmm OceanDNA-b12387/protein.faa > /dev/null
[2023-03-17 11:08:15,041] [INFO] Task succeeded: HMMsearch
[2023-03-17 11:08:15,041] [INFO] Found 6/6 markers.
[2023-03-17 11:08:15,062] [INFO] Query marker FASTA was written to OceanDNA-b12387/markers.fasta
[2023-03-17 11:08:15,063] [INFO] Task started: Blastn
[2023-03-17 11:08:15,063] [INFO] Running command: blastn -query OceanDNA-b12387/markers.fasta -db /var/lib/cwl/stg4601f105-adc2-4d47-8760-0d36f88bfe1c/dqc_reference/reference_markers.fasta -out OceanDNA-b12387/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:08:15,586] [INFO] Task succeeded: Blastn
[2023-03-17 11:08:15,591] [INFO] Selected 25 target genomes.
[2023-03-17 11:08:15,592] [INFO] Target genome list was writen to OceanDNA-b12387/target_genomes.txt
[2023-03-17 11:08:15,605] [INFO] Task started: fastANI
[2023-03-17 11:08:15,605] [INFO] Running command: fastANI --query /var/lib/cwl/stg299e4f95-3f98-40ad-9b93-6ae31ba1b943/OceanDNA-b12387.fa --refList OceanDNA-b12387/target_genomes.txt --output OceanDNA-b12387/fastani_result.tsv --threads 1
[2023-03-17 11:08:31,141] [INFO] Task succeeded: fastANI
[2023-03-17 11:08:31,142] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4601f105-adc2-4d47-8760-0d36f88bfe1c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 11:08:31,142] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4601f105-adc2-4d47-8760-0d36f88bfe1c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 11:08:31,145] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 11:08:31,145] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 11:08:31,145] [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
Vicingus serpentipes	strain=NCIMB 15042	GCA_007993035.1	1926625	1926625	type	True	75.1318	54	766	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 11:08:31,147] [INFO] DFAST Taxonomy check result was written to OceanDNA-b12387/tc_result.tsv
[2023-03-17 11:08:31,152] [INFO] ===== Taxonomy check completed =====
[2023-03-17 11:08:31,152] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 11:08:31,152] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4601f105-adc2-4d47-8760-0d36f88bfe1c/dqc_reference/checkm_data
[2023-03-17 11:08:31,153] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 11:08:31,160] [INFO] Task started: CheckM
[2023-03-17 11:08:31,160] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b12387/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b12387/checkm_input OceanDNA-b12387/checkm_result
[2023-03-17 11:09:08,053] [INFO] Task succeeded: CheckM
[2023-03-17 11:09:08,053] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 11:09:08,168] [INFO] ===== Completeness check finished =====
[2023-03-17 11:09:08,168] [INFO] ===== Start GTDB Search =====
[2023-03-17 11:09:08,168] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b12387/markers.fasta)
[2023-03-17 11:09:08,169] [INFO] Task started: Blastn
[2023-03-17 11:09:08,169] [INFO] Running command: blastn -query OceanDNA-b12387/markers.fasta -db /var/lib/cwl/stg4601f105-adc2-4d47-8760-0d36f88bfe1c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b12387/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 11:09:08,905] [INFO] Task succeeded: Blastn
[2023-03-17 11:09:08,916] [INFO] Selected 14 target genomes.
[2023-03-17 11:09:08,916] [INFO] Target genome list was writen to OceanDNA-b12387/target_genomes_gtdb.txt
[2023-03-17 11:09:09,067] [INFO] Task started: fastANI
[2023-03-17 11:09:09,068] [INFO] Running command: fastANI --query /var/lib/cwl/stg299e4f95-3f98-40ad-9b93-6ae31ba1b943/OceanDNA-b12387.fa --refList OceanDNA-b12387/target_genomes_gtdb.txt --output OceanDNA-b12387/fastani_result_gtdb.tsv --threads 1
[2023-03-17 11:09:14,262] [INFO] Task succeeded: fastANI
[2023-03-17 11:09:14,269] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 11:09:14,269] [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_002686655.1	s__MED-G20 sp002686655	82.8471	527	766	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__MED-G20	95.0	96.65	96.65	0.87	0.87	2	-
GCA_002457645.1	s__MED-G20 sp002457645	82.5113	305	766	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__MED-G20	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016780365.1	s__MED-G20 sp016780365	78.2749	277	766	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__MED-G20	95.0	98.18	97.06	0.79	0.71	6	-
GCA_905181675.1	s__MED-G20 sp905181675	78.213	233	766	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__MED-G20	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002713405.1	s__MED-G20 sp002713405	78.122	266	766	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__MED-G20	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002691605.1	s__MED-G20 sp002691605	78.1187	327	766	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__MED-G20	95.0	96.19	95.12	0.79	0.76	3	-
GCA_905182525.1	s__MED-G20 sp905182525	78.0655	277	766	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__MED-G20	95.0	96.07	96.07	0.86	0.86	2	-
GCA_002721285.1	s__SP287 sp002721285	76.7817	72	766	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__SP287	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902536695.1	s__GCA-002727735 sp902536695	76.125	75	766	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UBA10066;g__GCA-002727735	95.0	97.41	97.41	0.52	0.52	2	-
--------------------------------------------------------------------------------
[2023-03-17 11:09:14,272] [INFO] GTDB search result was written to OceanDNA-b12387/result_gtdb.tsv
[2023-03-17 11:09:14,276] [INFO] ===== GTDB Search completed =====
[2023-03-17 11:09:14,282] [INFO] DFAST_QC result json was written to OceanDNA-b12387/dqc_result.json
[2023-03-17 11:09:14,282] [INFO] DFAST_QC completed!
[2023-03-17 11:09:14,282] [INFO] Total running time: 0h1m14s