[2023-03-16 05:52:01,714] [INFO] DFAST_QC pipeline started.
[2023-03-16 05:52:01,714] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 05:52:01,714] [INFO] DQC Reference Directory: /var/lib/cwl/stge8ff9a9b-6dc4-47e5-8a88-e89fc446e76e/dqc_reference
[2023-03-16 05:52:02,820] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 05:52:02,820] [INFO] Task started: Prodigal
[2023-03-16 05:52:02,821] [INFO] Running command: cat /var/lib/cwl/stg4a4992cf-1379-4ae5-b547-6a00fbfc1205/OceanDNA-b34653.fa | prodigal -d OceanDNA-b34653/cds.fna -a OceanDNA-b34653/protein.faa -g 11 -q > /dev/null
[2023-03-16 05:52:29,505] [INFO] Task succeeded: Prodigal
[2023-03-16 05:52:29,505] [INFO] Task started: HMMsearch
[2023-03-16 05:52:29,505] [INFO] Running command: hmmsearch --tblout OceanDNA-b34653/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge8ff9a9b-6dc4-47e5-8a88-e89fc446e76e/dqc_reference/reference_markers.hmm OceanDNA-b34653/protein.faa > /dev/null
[2023-03-16 05:52:29,757] [INFO] Task succeeded: HMMsearch
[2023-03-16 05:52:29,757] [INFO] Found 6/6 markers.
[2023-03-16 05:52:29,786] [INFO] Query marker FASTA was written to OceanDNA-b34653/markers.fasta
[2023-03-16 05:52:29,787] [INFO] Task started: Blastn
[2023-03-16 05:52:29,787] [INFO] Running command: blastn -query OceanDNA-b34653/markers.fasta -db /var/lib/cwl/stge8ff9a9b-6dc4-47e5-8a88-e89fc446e76e/dqc_reference/reference_markers.fasta -out OceanDNA-b34653/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 05:52:30,457] [INFO] Task succeeded: Blastn
[2023-03-16 05:52:30,458] [INFO] Selected 12 target genomes.
[2023-03-16 05:52:30,459] [INFO] Target genome list was writen to OceanDNA-b34653/target_genomes.txt
[2023-03-16 05:52:30,464] [INFO] Task started: fastANI
[2023-03-16 05:52:30,465] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a4992cf-1379-4ae5-b547-6a00fbfc1205/OceanDNA-b34653.fa --refList OceanDNA-b34653/target_genomes.txt --output OceanDNA-b34653/fastani_result.tsv --threads 1
[2023-03-16 05:52:41,049] [INFO] Task succeeded: fastANI
[2023-03-16 05:52:41,049] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge8ff9a9b-6dc4-47e5-8a88-e89fc446e76e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 05:52:41,049] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge8ff9a9b-6dc4-47e5-8a88-e89fc446e76e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 05:52:41,057] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 05:52:41,057] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 05:52:41,057] [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
Colwellia marinimaniae	strain=MTCD1	GCA_002207865.1	1513592	1513592	type	True	85.0062	1050	1645	95	below_threshold
Colwellia piezophila	strain=ATCC BAA-637	GCA_000378625.1	211668	211668	type	True	83.9818	1023	1645	95	below_threshold
Colwellia demingiae	strain=ACAM 459	GCA_007954275.1	89401	89401	type	True	81.5505	898	1645	95	below_threshold
Colwellia ponticola	strain=OISW-25	GCA_005885605.1	2304625	2304625	type	True	80.128	602	1645	95	below_threshold
Colwellia echini	strain=A3	GCA_002843355.2	1982103	1982103	type	True	79.3926	522	1645	95	below_threshold
Colwellia hornerae	strain=ACAM 607	GCA_007954355.1	89402	89402	type	True	78.4907	292	1645	95	below_threshold
Litorilituus lipolyticus	strain=RZ04	GCA_006439335.1	2491017	2491017	type	True	78.2469	352	1645	95	below_threshold
Thalassomonas viridans	strain=XOM25	GCA_000948985.1	137584	137584	type	True	77.2683	101	1645	95	below_threshold
Photobacterium phosphoreum	strain=ATCC 11040	GCA_000949955.1	659	659	type	True	76.13	55	1645	95	below_threshold
Shewanella ulleungensis	strain=KCTC 62130	GCA_023283965.1	2282699	2282699	type	True	75.9257	75	1645	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 05:52:41,058] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34653/tc_result.tsv
[2023-03-16 05:52:41,058] [INFO] ===== Taxonomy check completed =====
[2023-03-16 05:52:41,058] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 05:52:41,058] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge8ff9a9b-6dc4-47e5-8a88-e89fc446e76e/dqc_reference/checkm_data
[2023-03-16 05:52:41,059] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 05:52:41,101] [INFO] Task started: CheckM
[2023-03-16 05:52:41,101] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34653/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34653/checkm_input OceanDNA-b34653/checkm_result
[2023-03-16 05:53:44,270] [INFO] Task succeeded: CheckM
[2023-03-16 05:53:44,270] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 05:53:44,275] [INFO] ===== Completeness check finished =====
[2023-03-16 05:53:44,276] [INFO] ===== Start GTDB Search =====
[2023-03-16 05:53:44,276] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34653/markers.fasta)
[2023-03-16 05:53:44,277] [INFO] Task started: Blastn
[2023-03-16 05:53:44,277] [INFO] Running command: blastn -query OceanDNA-b34653/markers.fasta -db /var/lib/cwl/stge8ff9a9b-6dc4-47e5-8a88-e89fc446e76e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34653/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 05:53:45,353] [INFO] Task succeeded: Blastn
[2023-03-16 05:53:45,355] [INFO] Selected 11 target genomes.
[2023-03-16 05:53:45,355] [INFO] Target genome list was writen to OceanDNA-b34653/target_genomes_gtdb.txt
[2023-03-16 05:53:45,366] [INFO] Task started: fastANI
[2023-03-16 05:53:45,366] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a4992cf-1379-4ae5-b547-6a00fbfc1205/OceanDNA-b34653.fa --refList OceanDNA-b34653/target_genomes_gtdb.txt --output OceanDNA-b34653/fastani_result_gtdb.tsv --threads 1
[2023-03-16 05:53:57,788] [INFO] Task succeeded: fastANI
[2023-03-16 05:53:57,795] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 05:53:57,795] [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_013214175.1	s__Colwellia sp013214175	99.991	1641	1645	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	95.17	95.17	0.89	0.89	2	conclusive
GCF_002207865.1	s__Colwellia marinimaniae	84.9798	1053	1645	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	99.40	98.81	0.97	0.94	3	-
GCF_001440345.1	s__Colwellia sp001440345	84.9706	1035	1645	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000378625.1	s__Colwellia piezophila	83.9762	1025	1645	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000764185.1	s__Colwellia psychrerythraea_B	83.6537	1173	1645	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002836255.1	s__Colwellia sp002836255	81.6383	990	1645	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002163005.1	s__Colwellia psychrerythraea_C	81.6171	800	1645	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007954275.1	s__Colwellia demingiae	81.566	896	1645	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003545415.1	s__Colwellia sp003545415	81.3783	625	1645	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000012325.1	s__Colwellia psychrerythraea_A	81.3529	898	1645	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	98.43	98.43	0.88	0.88	2	-
GCF_005885605.1	s__Colwellia ponticola	80.1273	604	1645	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 05:53:57,796] [INFO] GTDB search result was written to OceanDNA-b34653/result_gtdb.tsv
[2023-03-16 05:53:57,797] [INFO] ===== GTDB Search completed =====
[2023-03-16 05:53:57,800] [INFO] DFAST_QC result json was written to OceanDNA-b34653/dqc_result.json
[2023-03-16 05:53:57,800] [INFO] DFAST_QC completed!
[2023-03-16 05:53:57,800] [INFO] Total running time: 0h1m56s