[2023-03-18 06:37:01,797] [INFO] DFAST_QC pipeline started.
[2023-03-18 06:37:01,797] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 06:37:01,798] [INFO] DQC Reference Directory: /var/lib/cwl/stg0fd7fb5f-8a84-4a3b-ab84-17ea8f7aca23/dqc_reference
[2023-03-18 06:37:03,369] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 06:37:03,369] [INFO] Task started: Prodigal
[2023-03-18 06:37:03,369] [INFO] Running command: cat /var/lib/cwl/stgc57ac626-465f-42c1-b45d-d54c4ab118f8/OceanDNA-b22624.fa | prodigal -d OceanDNA-b22624/cds.fna -a OceanDNA-b22624/protein.faa -g 11 -q > /dev/null
[2023-03-18 06:37:24,511] [INFO] Task succeeded: Prodigal
[2023-03-18 06:37:24,511] [INFO] Task started: HMMsearch
[2023-03-18 06:37:24,511] [INFO] Running command: hmmsearch --tblout OceanDNA-b22624/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0fd7fb5f-8a84-4a3b-ab84-17ea8f7aca23/dqc_reference/reference_markers.hmm OceanDNA-b22624/protein.faa > /dev/null
[2023-03-18 06:37:24,700] [INFO] Task succeeded: HMMsearch
[2023-03-18 06:37:24,701] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgc57ac626-465f-42c1-b45d-d54c4ab118f8/OceanDNA-b22624.fa]
[2023-03-18 06:37:24,722] [INFO] Query marker FASTA was written to OceanDNA-b22624/markers.fasta
[2023-03-18 06:37:24,724] [INFO] Task started: Blastn
[2023-03-18 06:37:24,724] [INFO] Running command: blastn -query OceanDNA-b22624/markers.fasta -db /var/lib/cwl/stg0fd7fb5f-8a84-4a3b-ab84-17ea8f7aca23/dqc_reference/reference_markers.fasta -out OceanDNA-b22624/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 06:37:25,332] [INFO] Task succeeded: Blastn
[2023-03-18 06:37:25,333] [INFO] Selected 16 target genomes.
[2023-03-18 06:37:25,333] [INFO] Target genome list was writen to OceanDNA-b22624/target_genomes.txt
[2023-03-18 06:37:25,342] [INFO] Task started: fastANI
[2023-03-18 06:37:25,343] [INFO] Running command: fastANI --query /var/lib/cwl/stgc57ac626-465f-42c1-b45d-d54c4ab118f8/OceanDNA-b22624.fa --refList OceanDNA-b22624/target_genomes.txt --output OceanDNA-b22624/fastani_result.tsv --threads 1
[2023-03-18 06:37:41,509] [INFO] Task succeeded: fastANI
[2023-03-18 06:37:41,509] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0fd7fb5f-8a84-4a3b-ab84-17ea8f7aca23/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 06:37:41,509] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0fd7fb5f-8a84-4a3b-ab84-17ea8f7aca23/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 06:37:41,516] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 06:37:41,516] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 06:37:41,516] [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
Posidoniimonas corsicana	strain=KOR34	GCA_007859765.1	1938618	1938618	type	True	76.0298	135	1141	95	below_threshold
Posidoniimonas polymericola	strain=Pla123a	GCA_007859935.1	2528002	2528002	type	True	75.9343	148	1141	95	below_threshold
Botrimarina colliarenosi	strain=Pla108	GCA_007859955.1	2528001	2528001	type	True	75.9333	123	1141	95	below_threshold
Botrimarina mediterranea	strain=Spa11	GCA_007753265.1	2528022	2528022	type	True	75.919	120	1141	95	below_threshold
Pseudobythopirellula maris	strain=Mal64	GCA_007859945.1	2527991	2527991	type	True	75.9155	146	1141	95	below_threshold
Botrimarina hoheduenensis	strain=Pla111	GCA_007859815.1	2528000	2528000	type	True	75.8186	65	1141	95	below_threshold
Lacipirellula parvula	strain=PX69	GCA_009177095.1	2650471	2650471	type	True	75.4612	106	1141	95	below_threshold
Aeoliella mucimassa	strain=Pan181	GCA_007748035.1	2527972	2527972	type	True	75.3701	52	1141	95	below_threshold
Aquisphaera giovannonii	strain=OJF2	GCA_008087625.1	406548	406548	type	True	75.3178	216	1141	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 06:37:41,516] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22624/tc_result.tsv
[2023-03-18 06:37:41,517] [INFO] ===== Taxonomy check completed =====
[2023-03-18 06:37:41,517] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 06:37:41,517] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0fd7fb5f-8a84-4a3b-ab84-17ea8f7aca23/dqc_reference/checkm_data
[2023-03-18 06:37:41,517] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 06:37:41,522] [INFO] Task started: CheckM
[2023-03-18 06:37:41,522] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22624/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22624/checkm_input OceanDNA-b22624/checkm_result
[2023-03-18 06:38:59,473] [INFO] Task succeeded: CheckM
[2023-03-18 06:38:59,474] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.46%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 06:38:59,476] [INFO] ===== Completeness check finished =====
[2023-03-18 06:38:59,476] [INFO] ===== Start GTDB Search =====
[2023-03-18 06:38:59,477] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22624/markers.fasta)
[2023-03-18 06:38:59,478] [INFO] Task started: Blastn
[2023-03-18 06:38:59,478] [INFO] Running command: blastn -query OceanDNA-b22624/markers.fasta -db /var/lib/cwl/stg0fd7fb5f-8a84-4a3b-ab84-17ea8f7aca23/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22624/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 06:39:00,415] [INFO] Task succeeded: Blastn
[2023-03-18 06:39:00,415] [INFO] Selected 17 target genomes.
[2023-03-18 06:39:00,416] [INFO] Target genome list was writen to OceanDNA-b22624/target_genomes_gtdb.txt
[2023-03-18 06:39:00,672] [INFO] Task started: fastANI
[2023-03-18 06:39:00,672] [INFO] Running command: fastANI --query /var/lib/cwl/stgc57ac626-465f-42c1-b45d-d54c4ab118f8/OceanDNA-b22624.fa --refList OceanDNA-b22624/target_genomes_gtdb.txt --output OceanDNA-b22624/fastani_result_gtdb.tsv --threads 1
[2023-03-18 06:39:12,221] [INFO] Task succeeded: fastANI
[2023-03-18 06:39:12,231] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 06:39:12,231] [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_903917235.1	s__QWPN01 sp903917235	98.7355	944	1141	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	98.02	96.87	0.85	0.84	3	conclusive
GCA_010027105.1	s__RGVT01 sp010027105	79.1449	342	1141	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__RGVT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903919035.1	s__QWPN01 sp903919035	79.034	374	1141	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	99.57	99.56	0.90	0.89	5	-
GCA_903831155.1	s__QWPN01 sp903831155	79.0297	416	1141	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002405515.1	s__UBA4655 sp002405515	78.9584	386	1141	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__UBA4655	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014192425.1	s__QWPN01 sp014192425	78.9572	447	1141	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009926295.1	s__RGVT01 sp009926295	78.9458	367	1141	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__RGVT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016872925.1	s__QWPN01 sp016872925	78.9407	420	1141	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018970605.1	s__QWPN01 sp018970605	78.9173	357	1141	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003671185.1	s__QWPN01 sp003671185	78.6089	357	1141	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009923125.1	s__RGVT01 sp009923125	78.5173	267	1141	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__RGVT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005789975.1	s__QWPN01 sp005789975	78.3203	316	1141	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	99.49	99.44	0.83	0.81	3	-
GCA_009924545.1	s__F1-20-MAGs016 sp009924545	78.2352	399	1141	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__F1-20-MAGs016	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016872555.1	s__F1-20-MAGs016 sp016872555	78.0865	445	1141	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__F1-20-MAGs016	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898385.1	s__Paludisphaera sp001898385	75.3399	192	1141	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__Paludisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013696185.1	s__JACCZA01 sp013696185	74.6984	55	1141	d__Bacteria;p__Actinobacteriota;c__Thermoleophilia;o__Gaiellales;f__Gaiellaceae;g__JACCZA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016713225.1	s__JADJPO01 sp016713225	74.6763	58	1141	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Kineosporiaceae;g__JADJPO01	95.0	99.38	99.28	0.94	0.94	3	-
--------------------------------------------------------------------------------
[2023-03-18 06:39:12,232] [INFO] GTDB search result was written to OceanDNA-b22624/result_gtdb.tsv
[2023-03-18 06:39:12,232] [INFO] ===== GTDB Search completed =====
[2023-03-18 06:39:12,233] [INFO] DFAST_QC result json was written to OceanDNA-b22624/dqc_result.json
[2023-03-18 06:39:12,233] [INFO] DFAST_QC completed!
[2023-03-18 06:39:12,233] [INFO] Total running time: 0h2m10s