[2023-03-16 18:51:07,845] [INFO] DFAST_QC pipeline started.
[2023-03-16 18:51:07,845] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 18:51:07,845] [INFO] DQC Reference Directory: /var/lib/cwl/stgd2b5f9d9-3a75-4302-b044-21668237304d/dqc_reference
[2023-03-16 18:51:08,989] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 18:51:08,989] [INFO] Task started: Prodigal
[2023-03-16 18:51:08,989] [INFO] Running command: cat /var/lib/cwl/stgcc390106-f170-42d7-9641-2bd08bdd61e2/OceanDNA-b35208.fa | prodigal -d OceanDNA-b35208/cds.fna -a OceanDNA-b35208/protein.faa -g 11 -q > /dev/null
[2023-03-16 18:51:34,650] [INFO] Task succeeded: Prodigal
[2023-03-16 18:51:34,651] [INFO] Task started: HMMsearch
[2023-03-16 18:51:34,651] [INFO] Running command: hmmsearch --tblout OceanDNA-b35208/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd2b5f9d9-3a75-4302-b044-21668237304d/dqc_reference/reference_markers.hmm OceanDNA-b35208/protein.faa > /dev/null
[2023-03-16 18:51:34,904] [INFO] Task succeeded: HMMsearch
[2023-03-16 18:51:34,904] [INFO] Found 6/6 markers.
[2023-03-16 18:51:34,931] [INFO] Query marker FASTA was written to OceanDNA-b35208/markers.fasta
[2023-03-16 18:51:34,932] [INFO] Task started: Blastn
[2023-03-16 18:51:34,932] [INFO] Running command: blastn -query OceanDNA-b35208/markers.fasta -db /var/lib/cwl/stgd2b5f9d9-3a75-4302-b044-21668237304d/dqc_reference/reference_markers.fasta -out OceanDNA-b35208/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:51:35,611] [INFO] Task succeeded: Blastn
[2023-03-16 18:51:35,612] [INFO] Selected 10 target genomes.
[2023-03-16 18:51:35,612] [INFO] Target genome list was writen to OceanDNA-b35208/target_genomes.txt
[2023-03-16 18:51:35,619] [INFO] Task started: fastANI
[2023-03-16 18:51:35,619] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc390106-f170-42d7-9641-2bd08bdd61e2/OceanDNA-b35208.fa --refList OceanDNA-b35208/target_genomes.txt --output OceanDNA-b35208/fastani_result.tsv --threads 1
[2023-03-16 18:51:44,295] [INFO] Task succeeded: fastANI
[2023-03-16 18:51:44,296] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd2b5f9d9-3a75-4302-b044-21668237304d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 18:51:44,296] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd2b5f9d9-3a75-4302-b044-21668237304d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 18:51:44,303] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 18:51:44,303] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 18:51:44,303] [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
Moritella yayanosii	strain=DB21MT 5	GCA_900465055.1	69539	69539	type	True	93.1544	1195	1580	95	below_threshold
Moritella dasanensis	strain=ArB 0140	GCA_000276805.1	428031	428031	type	True	84.8816	1107	1580	95	below_threshold
Moritella marina	strain=MP-1	GCA_008931805.1	90736	90736	type	True	83.8274	1023	1580	95	below_threshold
Moritella marina	strain=ATCC 15381	GCA_000291685.1	90736	90736	type	True	83.7789	997	1580	95	below_threshold
Moritella marina	strain=MP-1	GCA_000381865.1	90736	90736	type	True	83.7323	1020	1580	95	below_threshold
Vibrio cortegadensis	strain=CECT 7227	GCA_024347395.1	1328770	1328770	type	True	76.8101	84	1580	95	below_threshold
Motilimonas eburnea	strain=YH6	GCA_021295345.1	1737488	1737488	type	True	76.6169	58	1580	95	below_threshold
Pseudoalteromonas rhizosphaerae	strain=RA15	GCA_902498845.1	2518973	2518973	type	True	76.5645	63	1580	95	below_threshold
Photobacterium toruni	strain=CECT 9189	GCA_024529955.1	1935446	1935446	type	True	76.5633	76	1580	95	below_threshold
Shewanella inventionis	strain=KCTC 42807	GCA_023283595.1	1738770	1738770	type	True	76.3852	53	1580	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 18:51:44,303] [INFO] DFAST Taxonomy check result was written to OceanDNA-b35208/tc_result.tsv
[2023-03-16 18:51:44,303] [INFO] ===== Taxonomy check completed =====
[2023-03-16 18:51:44,304] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 18:51:44,304] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd2b5f9d9-3a75-4302-b044-21668237304d/dqc_reference/checkm_data
[2023-03-16 18:51:44,304] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 18:51:44,407] [INFO] Task started: CheckM
[2023-03-16 18:51:44,407] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b35208/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b35208/checkm_input OceanDNA-b35208/checkm_result
[2023-03-16 18:53:06,160] [INFO] Task succeeded: CheckM
[2023-03-16 18:53:06,161] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 18:53:06,164] [INFO] ===== Completeness check finished =====
[2023-03-16 18:53:06,164] [INFO] ===== Start GTDB Search =====
[2023-03-16 18:53:06,164] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b35208/markers.fasta)
[2023-03-16 18:53:06,165] [INFO] Task started: Blastn
[2023-03-16 18:53:06,165] [INFO] Running command: blastn -query OceanDNA-b35208/markers.fasta -db /var/lib/cwl/stgd2b5f9d9-3a75-4302-b044-21668237304d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b35208/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:53:07,221] [INFO] Task succeeded: Blastn
[2023-03-16 18:53:07,222] [INFO] Selected 7 target genomes.
[2023-03-16 18:53:07,222] [INFO] Target genome list was writen to OceanDNA-b35208/target_genomes_gtdb.txt
[2023-03-16 18:53:07,230] [INFO] Task started: fastANI
[2023-03-16 18:53:07,231] [INFO] Running command: fastANI --query /var/lib/cwl/stgcc390106-f170-42d7-9641-2bd08bdd61e2/OceanDNA-b35208.fa --refList OceanDNA-b35208/target_genomes_gtdb.txt --output OceanDNA-b35208/fastani_result_gtdb.tsv --threads 1
[2023-03-16 18:53:15,609] [INFO] Task succeeded: fastANI
[2023-03-16 18:53:15,614] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 18:53:15,614] [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_013215705.1	s__Moritella sp013215705	99.9668	1515	1580	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Moritellaceae;g__Moritella	95.0	95.77	95.77	0.82	0.82	2	conclusive
GCF_000170855.1	s__Moritella sp000170855	93.8025	1271	1580	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Moritellaceae;g__Moritella	95.0	97.45	95.37	0.88	0.83	4	-
GCF_900465055.1	s__Moritella yayanosii	93.1451	1196	1580	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Moritellaceae;g__Moritella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001574435.1	s__Moritella sp001574435	87.9996	1148	1580	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Moritellaceae;g__Moritella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018219455.1	s__Moritella sp018219455	86.8741	1166	1580	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Moritellaceae;g__Moritella	95.0	96.81	96.78	0.88	0.87	3	-
GCA_000953735.1	s__Moritella viscosa	86.8405	1180	1580	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Moritellaceae;g__Moritella	95.0	99.48	99.13	0.93	0.91	13	-
GCF_018219155.1	s__Moritella sp018219155	84.0202	1002	1580	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Moritellaceae;g__Moritella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 18:53:15,614] [INFO] GTDB search result was written to OceanDNA-b35208/result_gtdb.tsv
[2023-03-16 18:53:15,615] [INFO] ===== GTDB Search completed =====
[2023-03-16 18:53:15,616] [INFO] DFAST_QC result json was written to OceanDNA-b35208/dqc_result.json
[2023-03-16 18:53:15,616] [INFO] DFAST_QC completed!
[2023-03-16 18:53:15,616] [INFO] Total running time: 0h2m8s