[2023-03-18 00:58:44,632] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:58:44,633] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:58:44,633] [INFO] DQC Reference Directory: /var/lib/cwl/stgbfaf325c-142d-4623-b732-eec5c9187b1f/dqc_reference
[2023-03-18 00:58:46,296] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:58:46,296] [INFO] Task started: Prodigal
[2023-03-18 00:58:46,297] [INFO] Running command: cat /var/lib/cwl/stg5b0de377-75d8-4a99-89d1-554bef258b7a/OceanDNA-b6452.fa | prodigal -d OceanDNA-b6452/cds.fna -a OceanDNA-b6452/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:59:06,944] [INFO] Task succeeded: Prodigal
[2023-03-18 00:59:06,944] [INFO] Task started: HMMsearch
[2023-03-18 00:59:06,944] [INFO] Running command: hmmsearch --tblout OceanDNA-b6452/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbfaf325c-142d-4623-b732-eec5c9187b1f/dqc_reference/reference_markers.hmm OceanDNA-b6452/protein.faa > /dev/null
[2023-03-18 00:59:07,148] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:59:07,148] [INFO] Found 6/6 markers.
[2023-03-18 00:59:07,172] [INFO] Query marker FASTA was written to OceanDNA-b6452/markers.fasta
[2023-03-18 00:59:07,173] [INFO] Task started: Blastn
[2023-03-18 00:59:07,173] [INFO] Running command: blastn -query OceanDNA-b6452/markers.fasta -db /var/lib/cwl/stgbfaf325c-142d-4623-b732-eec5c9187b1f/dqc_reference/reference_markers.fasta -out OceanDNA-b6452/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:59:07,757] [INFO] Task succeeded: Blastn
[2023-03-18 00:59:07,781] [INFO] Selected 11 target genomes.
[2023-03-18 00:59:07,782] [INFO] Target genome list was writen to OceanDNA-b6452/target_genomes.txt
[2023-03-18 00:59:07,786] [INFO] Task started: fastANI
[2023-03-18 00:59:07,786] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b0de377-75d8-4a99-89d1-554bef258b7a/OceanDNA-b6452.fa --refList OceanDNA-b6452/target_genomes.txt --output OceanDNA-b6452/fastani_result.tsv --threads 1
[2023-03-18 00:59:15,302] [INFO] Task succeeded: fastANI
[2023-03-18 00:59:15,302] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbfaf325c-142d-4623-b732-eec5c9187b1f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 00:59:15,302] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbfaf325c-142d-4623-b732-eec5c9187b1f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 00:59:15,310] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 00:59:15,310] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 00:59:15,310] [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
Aequorivita iocasae	strain=KX20305	GCA_016757735.1	2803865	2803865	type	True	87.5652	746	936	95	below_threshold
Aequorivita aquimaris	strain=D-24	GCA_001573155.1	1548749	1548749	type	True	86.0511	766	936	95	below_threshold
Aequorivita vladivostokensis	strain=KMM 3516	GCA_000952855.1	171194	171194	type	True	82.5386	704	936	95	below_threshold
Aequorivita soesokkakensis	strain=RSSK-12	GCA_001641085.1	1385699	1385699	type	True	81.4339	644	936	95	below_threshold
Aequorivita antarctica	strain=SW49	GCA_007997155.1	153266	153266	type	True	80.4911	601	936	95	below_threshold
Aequorivita lipolytica	strain=Y10-2	GCA_007997135.1	153267	153267	type	True	80.3872	616	936	95	below_threshold
Aequorivita sublithincola	strain=DSM 14238	GCA_000265385.1	101385	101385	type	True	79.332	558	936	95	below_threshold
Halomarinibacterium sedimenti	strain=CAU 1614	GCA_019312585.1	2857106	2857106	type	True	76.8421	129	936	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	76.4387	57	936	95	below_threshold
Hyunsoonleella aquatilis	strain=SJ7	GCA_014270105.1	2762758	2762758	type	True	76.3429	60	936	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	75.908	58	936	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 00:59:15,312] [INFO] DFAST Taxonomy check result was written to OceanDNA-b6452/tc_result.tsv
[2023-03-18 00:59:15,312] [INFO] ===== Taxonomy check completed =====
[2023-03-18 00:59:15,312] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:59:15,312] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbfaf325c-142d-4623-b732-eec5c9187b1f/dqc_reference/checkm_data
[2023-03-18 00:59:15,313] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:59:15,335] [INFO] Task started: CheckM
[2023-03-18 00:59:15,335] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b6452/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b6452/checkm_input OceanDNA-b6452/checkm_result
[2023-03-18 01:00:08,173] [INFO] Task succeeded: CheckM
[2023-03-18 01:00:08,173] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 01:00:08,180] [INFO] ===== Completeness check finished =====
[2023-03-18 01:00:08,180] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:00:08,180] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b6452/markers.fasta)
[2023-03-18 01:00:08,181] [INFO] Task started: Blastn
[2023-03-18 01:00:08,181] [INFO] Running command: blastn -query OceanDNA-b6452/markers.fasta -db /var/lib/cwl/stgbfaf325c-142d-4623-b732-eec5c9187b1f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b6452/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:00:08,999] [INFO] Task succeeded: Blastn
[2023-03-18 01:00:09,002] [INFO] Selected 7 target genomes.
[2023-03-18 01:00:09,002] [INFO] Target genome list was writen to OceanDNA-b6452/target_genomes_gtdb.txt
[2023-03-18 01:00:09,008] [INFO] Task started: fastANI
[2023-03-18 01:00:09,008] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b0de377-75d8-4a99-89d1-554bef258b7a/OceanDNA-b6452.fa --refList OceanDNA-b6452/target_genomes_gtdb.txt --output OceanDNA-b6452/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:00:14,133] [INFO] Task succeeded: fastANI
[2023-03-18 01:00:14,138] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 01:00:14,138] [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_002715485.1	s__Aequorivita sp002715485	99.4474	811	936	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	99.49	99.49	0.87	0.87	2	conclusive
GCF_016757735.1	s__Aequorivita sp016757735	87.5796	744	936	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002364215.1	s__Aequorivita sp002364215	87.1361	782	936	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	99.66	98.55	0.97	0.89	12	-
GCA_002733915.1	s__Aequorivita sp002733915	86.7124	742	936	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001573155.1	s__Aequorivita aquimaris	86.0511	766	936	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000952855.1	s__Aequorivita vladivostokensis	82.5502	703	936	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	98.24	98.00	0.93	0.90	7	-
GCF_001641085.1	s__Aequorivita soesokkakensis	81.4442	643	936	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	97.26	97.26	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2023-03-18 01:00:14,139] [INFO] GTDB search result was written to OceanDNA-b6452/result_gtdb.tsv
[2023-03-18 01:00:14,139] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:00:14,141] [INFO] DFAST_QC result json was written to OceanDNA-b6452/dqc_result.json
[2023-03-18 01:00:14,141] [INFO] DFAST_QC completed!
[2023-03-18 01:00:14,141] [INFO] Total running time: 0h1m30s