[2023-03-14 13:36:05,688] [INFO] DFAST_QC pipeline started.
[2023-03-14 13:36:05,688] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 13:36:05,688] [INFO] DQC Reference Directory: /var/lib/cwl/stga915fc96-58af-4e96-bc2a-103cdb9c6223/dqc_reference
[2023-03-14 13:36:06,806] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 13:36:06,806] [INFO] Task started: Prodigal
[2023-03-14 13:36:06,806] [INFO] Running command: cat /var/lib/cwl/stg753c98d8-0814-4cc5-866e-2b586de6ea02/OceanDNA-b34760.fa | prodigal -d OceanDNA-b34760/cds.fna -a OceanDNA-b34760/protein.faa -g 11 -q > /dev/null
[2023-03-14 13:36:19,900] [INFO] Task succeeded: Prodigal
[2023-03-14 13:36:19,900] [INFO] Task started: HMMsearch
[2023-03-14 13:36:19,900] [INFO] Running command: hmmsearch --tblout OceanDNA-b34760/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga915fc96-58af-4e96-bc2a-103cdb9c6223/dqc_reference/reference_markers.hmm OceanDNA-b34760/protein.faa > /dev/null
[2023-03-14 13:36:20,118] [INFO] Task succeeded: HMMsearch
[2023-03-14 13:36:20,119] [INFO] Found 6/6 markers.
[2023-03-14 13:36:20,143] [INFO] Query marker FASTA was written to OceanDNA-b34760/markers.fasta
[2023-03-14 13:36:20,144] [INFO] Task started: Blastn
[2023-03-14 13:36:20,144] [INFO] Running command: blastn -query OceanDNA-b34760/markers.fasta -db /var/lib/cwl/stga915fc96-58af-4e96-bc2a-103cdb9c6223/dqc_reference/reference_markers.fasta -out OceanDNA-b34760/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:36:20,808] [INFO] Task succeeded: Blastn
[2023-03-14 13:36:20,809] [INFO] Selected 11 target genomes.
[2023-03-14 13:36:20,809] [INFO] Target genome list was writen to OceanDNA-b34760/target_genomes.txt
[2023-03-14 13:36:20,816] [INFO] Task started: fastANI
[2023-03-14 13:36:20,816] [INFO] Running command: fastANI --query /var/lib/cwl/stg753c98d8-0814-4cc5-866e-2b586de6ea02/OceanDNA-b34760.fa --refList OceanDNA-b34760/target_genomes.txt --output OceanDNA-b34760/fastani_result.tsv --threads 1
[2023-03-14 13:36:31,447] [INFO] Task succeeded: fastANI
[2023-03-14 13:36:31,448] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga915fc96-58af-4e96-bc2a-103cdb9c6223/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 13:36:31,448] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga915fc96-58af-4e96-bc2a-103cdb9c6223/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 13:36:31,454] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 13:36:31,454] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-14 13:36:31,454] [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 demingiae	strain=ACAM 459	GCA_007954275.1	89401	89401	type	True	82.8013	567	766	95	below_threshold
Colwellia piezophila	strain=ATCC BAA-637	GCA_000378625.1	211668	211668	type	True	80.2851	490	766	95	below_threshold
Colwellia marinimaniae	strain=MTCD1	GCA_002207865.1	1513592	1513592	type	True	80.2583	495	766	95	below_threshold
Colwellia ponticola	strain=OISW-25	GCA_005885605.1	2304625	2304625	type	True	80.1878	416	766	95	below_threshold
Colwellia echini	strain=A3	GCA_002843355.2	1982103	1982103	type	True	79.0084	330	766	95	below_threshold
Litorilituus lipolyticus	strain=RZ04	GCA_006439335.1	2491017	2491017	type	True	77.6854	191	766	95	below_threshold
Cognaticolwellia mytili	strain=KCTC 52417	GCA_002104475.1	1888913	1888913	type	True	77.2715	139	766	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-14 13:36:31,454] [INFO] DFAST Taxonomy check result was written to OceanDNA-b34760/tc_result.tsv
[2023-03-14 13:36:31,454] [INFO] ===== Taxonomy check completed =====
[2023-03-14 13:36:31,454] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 13:36:31,455] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga915fc96-58af-4e96-bc2a-103cdb9c6223/dqc_reference/checkm_data
[2023-03-14 13:36:31,455] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 13:36:31,460] [INFO] Task started: CheckM
[2023-03-14 13:36:31,460] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b34760/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b34760/checkm_input OceanDNA-b34760/checkm_result
[2023-03-14 13:37:15,140] [INFO] Task succeeded: CheckM
[2023-03-14 13:37:15,140] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-14 13:37:15,143] [INFO] ===== Completeness check finished =====
[2023-03-14 13:37:15,143] [INFO] ===== Start GTDB Search =====
[2023-03-14 13:37:15,143] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b34760/markers.fasta)
[2023-03-14 13:37:15,144] [INFO] Task started: Blastn
[2023-03-14 13:37:15,145] [INFO] Running command: blastn -query OceanDNA-b34760/markers.fasta -db /var/lib/cwl/stga915fc96-58af-4e96-bc2a-103cdb9c6223/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b34760/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 13:37:16,410] [INFO] Task succeeded: Blastn
[2023-03-14 13:37:16,411] [INFO] Selected 6 target genomes.
[2023-03-14 13:37:16,411] [INFO] Target genome list was writen to OceanDNA-b34760/target_genomes_gtdb.txt
[2023-03-14 13:37:16,415] [INFO] Task started: fastANI
[2023-03-14 13:37:16,415] [INFO] Running command: fastANI --query /var/lib/cwl/stg753c98d8-0814-4cc5-866e-2b586de6ea02/OceanDNA-b34760.fa --refList OceanDNA-b34760/target_genomes_gtdb.txt --output OceanDNA-b34760/fastani_result_gtdb.tsv --threads 1
[2023-03-14 13:37:22,334] [INFO] Task succeeded: fastANI
[2023-03-14 13:37:22,339] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 13:37:22,339] [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_003545415.1	s__Colwellia sp003545415	95.4131	576	766	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002836255.1	s__Colwellia sp002836255	87.894	642	766	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002836775.1	s__Colwellia sp002836775	86.3818	637	766	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	82.8427	557	766	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	98.43	98.43	0.88	0.88	2	-
GCA_002163005.1	s__Colwellia psychrerythraea_C	82.8293	505	766	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	82.7965	568	766	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Colwellia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 13:37:22,339] [INFO] GTDB search result was written to OceanDNA-b34760/result_gtdb.tsv
[2023-03-14 13:37:22,340] [INFO] ===== GTDB Search completed =====
[2023-03-14 13:37:22,341] [INFO] DFAST_QC result json was written to OceanDNA-b34760/dqc_result.json
[2023-03-14 13:37:22,341] [INFO] DFAST_QC completed!
[2023-03-14 13:37:22,341] [INFO] Total running time: 0h1m17s