[2023-06-30 00:21:16,387] [INFO] DFAST_QC pipeline started.
[2023-06-30 00:21:16,389] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 00:21:16,390] [INFO] DQC Reference Directory: /var/lib/cwl/stg64760544-f69d-41ba-b398-686ba3bdf043/dqc_reference
[2023-06-30 00:21:17,618] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 00:21:17,619] [INFO] Task started: Prodigal
[2023-06-30 00:21:17,620] [INFO] Running command: gunzip -c /var/lib/cwl/stgef8a7457-fd53-4aff-805b-b1bfe0180590/GCA_016868645.1_JGI_2017-08-21_genomic.fna.gz | prodigal -d GCA_016868645.1_JGI_2017-08-21_genomic.fna/cds.fna -a GCA_016868645.1_JGI_2017-08-21_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 00:21:25,666] [INFO] Task succeeded: Prodigal
[2023-06-30 00:21:25,667] [INFO] Task started: HMMsearch
[2023-06-30 00:21:25,667] [INFO] Running command: hmmsearch --tblout GCA_016868645.1_JGI_2017-08-21_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg64760544-f69d-41ba-b398-686ba3bdf043/dqc_reference/reference_markers.hmm GCA_016868645.1_JGI_2017-08-21_genomic.fna/protein.faa > /dev/null
[2023-06-30 00:21:25,880] [INFO] Task succeeded: HMMsearch
[2023-06-30 00:21:25,882] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgef8a7457-fd53-4aff-805b-b1bfe0180590/GCA_016868645.1_JGI_2017-08-21_genomic.fna.gz]
[2023-06-30 00:21:25,907] [INFO] Query marker FASTA was written to GCA_016868645.1_JGI_2017-08-21_genomic.fna/markers.fasta
[2023-06-30 00:21:25,908] [INFO] Task started: Blastn
[2023-06-30 00:21:25,908] [INFO] Running command: blastn -query GCA_016868645.1_JGI_2017-08-21_genomic.fna/markers.fasta -db /var/lib/cwl/stg64760544-f69d-41ba-b398-686ba3bdf043/dqc_reference/reference_markers.fasta -out GCA_016868645.1_JGI_2017-08-21_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 00:21:26,405] [INFO] Task succeeded: Blastn
[2023-06-30 00:21:26,409] [INFO] Selected 16 target genomes.
[2023-06-30 00:21:26,409] [INFO] Target genome list was writen to GCA_016868645.1_JGI_2017-08-21_genomic.fna/target_genomes.txt
[2023-06-30 00:21:26,411] [INFO] Task started: fastANI
[2023-06-30 00:21:26,411] [INFO] Running command: fastANI --query /var/lib/cwl/stgef8a7457-fd53-4aff-805b-b1bfe0180590/GCA_016868645.1_JGI_2017-08-21_genomic.fna.gz --refList GCA_016868645.1_JGI_2017-08-21_genomic.fna/target_genomes.txt --output GCA_016868645.1_JGI_2017-08-21_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 00:21:37,254] [INFO] Task succeeded: fastANI
[2023-06-30 00:21:37,254] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg64760544-f69d-41ba-b398-686ba3bdf043/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 00:21:37,254] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg64760544-f69d-41ba-b398-686ba3bdf043/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 00:21:37,263] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 00:21:37,263] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 00:21:37,263] [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
Algoriphagus sanaruensis	strain=M8-2	GCA_001593605.1	1727163	1727163	type	True	77.3315	60	296	95	below_threshold
Algoriphagus boseongensis	strain=CECT 8446	GCA_004362805.1	1442587	1442587	type	True	77.245	56	296	95	below_threshold
Algoriphagus aestuariicola	strain=JCM 31546	GCA_017254835.1	1852016	1852016	type	True	77.0021	55	296	95	below_threshold
Algoriphagus alkaliphilus	strain=DSM 22703	GCA_900103735.1	279824	279824	type	True	76.9012	58	296	95	below_threshold
Algoriphagus litoralis	strain=DSL-12	GCA_003259255.1	2202829	2202829	type	True	76.8668	59	296	95	below_threshold
Algoriphagus lacus	strain=N3	GCA_003583985.1	2056311	2056311	type	True	76.8298	77	296	95	below_threshold
Algoriphagus mannitolivorans	strain=DSM 15301	GCA_000429425.1	226504	226504	type	True	76.713	69	296	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 00:21:37,266] [INFO] DFAST Taxonomy check result was written to GCA_016868645.1_JGI_2017-08-21_genomic.fna/tc_result.tsv
[2023-06-30 00:21:37,266] [INFO] ===== Taxonomy check completed =====
[2023-06-30 00:21:37,267] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 00:21:37,267] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg64760544-f69d-41ba-b398-686ba3bdf043/dqc_reference/checkm_data
[2023-06-30 00:21:37,268] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 00:21:37,292] [INFO] Task started: CheckM
[2023-06-30 00:21:37,293] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016868645.1_JGI_2017-08-21_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016868645.1_JGI_2017-08-21_genomic.fna/checkm_input GCA_016868645.1_JGI_2017-08-21_genomic.fna/checkm_result
[2023-06-30 00:22:05,765] [INFO] Task succeeded: CheckM
[2023-06-30 00:22:05,766] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.79%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 00:22:05,787] [INFO] ===== Completeness check finished =====
[2023-06-30 00:22:05,787] [INFO] ===== Start GTDB Search =====
[2023-06-30 00:22:05,788] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016868645.1_JGI_2017-08-21_genomic.fna/markers.fasta)
[2023-06-30 00:22:05,788] [INFO] Task started: Blastn
[2023-06-30 00:22:05,788] [INFO] Running command: blastn -query GCA_016868645.1_JGI_2017-08-21_genomic.fna/markers.fasta -db /var/lib/cwl/stg64760544-f69d-41ba-b398-686ba3bdf043/dqc_reference/reference_markers_gtdb.fasta -out GCA_016868645.1_JGI_2017-08-21_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 00:22:06,244] [INFO] Task succeeded: Blastn
[2023-06-30 00:22:06,249] [INFO] Selected 14 target genomes.
[2023-06-30 00:22:06,249] [INFO] Target genome list was writen to GCA_016868645.1_JGI_2017-08-21_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 00:22:06,254] [INFO] Task started: fastANI
[2023-06-30 00:22:06,254] [INFO] Running command: fastANI --query /var/lib/cwl/stgef8a7457-fd53-4aff-805b-b1bfe0180590/GCA_016868645.1_JGI_2017-08-21_genomic.fna.gz --refList GCA_016868645.1_JGI_2017-08-21_genomic.fna/target_genomes_gtdb.txt --output GCA_016868645.1_JGI_2017-08-21_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 00:22:14,561] [INFO] Task succeeded: fastANI
[2023-06-30 00:22:14,573] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 00:22:14,573] [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_903952135.1	s__Algoriphagus sp903952135	85.464	272	296	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	99.47	99.47	0.91	0.91	2	-
GCA_005788235.1	s__Algoriphagus sp005788235	80.4026	195	296	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016866385.1	s__Algoriphagus sp016866385	80.2035	112	296	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014324365.1	s__Algoriphagus sp014324365	77.3319	82	296	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001593605.1	s__Algoriphagus sanaruensis	77.3315	60	296	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362805.1	s__Algoriphagus boseongensis	77.245	56	296	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103735.1	s__Algoriphagus alkaliphilus	76.9012	58	296	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	99.41	99.41	0.93	0.93	2	-
GCF_003583985.1	s__Algoriphagus lacus	76.8298	77	296	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 00:22:14,575] [INFO] GTDB search result was written to GCA_016868645.1_JGI_2017-08-21_genomic.fna/result_gtdb.tsv
[2023-06-30 00:22:14,576] [INFO] ===== GTDB Search completed =====
[2023-06-30 00:22:14,580] [INFO] DFAST_QC result json was written to GCA_016868645.1_JGI_2017-08-21_genomic.fna/dqc_result.json
[2023-06-30 00:22:14,580] [INFO] DFAST_QC completed!
[2023-06-30 00:22:14,580] [INFO] Total running time: 0h0m58s