[2023-03-16 06:57:27,876] [INFO] DFAST_QC pipeline started.
[2023-03-16 06:57:27,876] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 06:57:27,876] [INFO] DQC Reference Directory: /var/lib/cwl/stg11704a55-b3a7-4261-a1dc-c8602122ce6f/dqc_reference
[2023-03-16 06:57:28,973] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 06:57:28,973] [INFO] Task started: Prodigal
[2023-03-16 06:57:28,973] [INFO] Running command: cat /var/lib/cwl/stg7b3e7142-5627-4e5b-8e44-0cdbfbae621e/OceanDNA-b33279.fa | prodigal -d OceanDNA-b33279/cds.fna -a OceanDNA-b33279/protein.faa -g 11 -q > /dev/null
[2023-03-16 06:57:41,253] [INFO] Task succeeded: Prodigal
[2023-03-16 06:57:41,254] [INFO] Task started: HMMsearch
[2023-03-16 06:57:41,254] [INFO] Running command: hmmsearch --tblout OceanDNA-b33279/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg11704a55-b3a7-4261-a1dc-c8602122ce6f/dqc_reference/reference_markers.hmm OceanDNA-b33279/protein.faa > /dev/null
[2023-03-16 06:57:41,421] [INFO] Task succeeded: HMMsearch
[2023-03-16 06:57:41,421] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg7b3e7142-5627-4e5b-8e44-0cdbfbae621e/OceanDNA-b33279.fa]
[2023-03-16 06:57:41,436] [INFO] Query marker FASTA was written to OceanDNA-b33279/markers.fasta
[2023-03-16 06:57:41,437] [INFO] Task started: Blastn
[2023-03-16 06:57:41,437] [INFO] Running command: blastn -query OceanDNA-b33279/markers.fasta -db /var/lib/cwl/stg11704a55-b3a7-4261-a1dc-c8602122ce6f/dqc_reference/reference_markers.fasta -out OceanDNA-b33279/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:57:41,954] [INFO] Task succeeded: Blastn
[2023-03-16 06:57:41,954] [INFO] Selected 15 target genomes.
[2023-03-16 06:57:41,954] [INFO] Target genome list was writen to OceanDNA-b33279/target_genomes.txt
[2023-03-16 06:57:41,975] [INFO] Task started: fastANI
[2023-03-16 06:57:41,975] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b3e7142-5627-4e5b-8e44-0cdbfbae621e/OceanDNA-b33279.fa --refList OceanDNA-b33279/target_genomes.txt --output OceanDNA-b33279/fastani_result.tsv --threads 1
[2023-03-16 06:57:52,812] [INFO] Task succeeded: fastANI
[2023-03-16 06:57:52,812] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg11704a55-b3a7-4261-a1dc-c8602122ce6f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 06:57:52,812] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg11704a55-b3a7-4261-a1dc-c8602122ce6f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 06:57:52,864] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 06:57:52,865] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 06:57:52,865] [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
Ideonella dechloratans	strain=CCUG 30977	GCA_008801845.1	36863	36863	type	True	79.4916	278	620	95	below_threshold
Ideonella dechloratans	strain=CCUG 30977	GCA_021049305.1	36863	36863	type	True	79.4416	275	620	95	below_threshold
Azohydromonas australica	strain=DSM 1124	GCA_000430725.1	364039	364039	type	True	79.4389	311	620	95	below_threshold
Azohydromonas caseinilytica	strain=G-1-1-14	GCA_012927045.1	2728836	2728836	type	True	79.171	313	620	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_015476235.1	215580	215580	type	True	79.0009	273	620	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_002933415.1	215580	215580	type	True	78.9285	278	620	95	below_threshold
Schlegelella thermodepolymerans	strain=DSM 15344	GCA_003349825.1	215580	215580	type	True	78.9182	275	620	95	below_threshold
Sphaerotilus hippei	strain=DSM 566	GCA_003201595.1	744406	744406	type	True	78.8831	260	620	95	below_threshold
Ideonella livida	strain=TBM-1	GCA_010499455.1	2707176	2707176	type	True	78.8533	293	620	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000190375.2	316997	316997	type	True	78.8089	265	620	95	below_threshold
Sphaerotilus natans subsp. natans	strain=DSM 6575	GCA_000689195.1	882627	34103	type	True	78.7389	271	620	95	below_threshold
Sphaerotilus natans	strain=ATCC 13338	GCA_900156335.1	34103	34103	type	True	78.6928	285	620	95	below_threshold
Sphaerotilus montanus	strain=HS	GCA_013426955.1	522889	522889	type	True	78.3541	260	620	95	below_threshold
Sphaerotilus montanus	strain=DSM 21226	GCA_013410775.1	522889	522889	type	True	78.3216	268	620	95	below_threshold
Rhizobacter gummiphilus	strain=NBRC 109400	GCA_002762215.1	946333	946333	type	True	78.2685	250	620	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 06:57:52,865] [INFO] DFAST Taxonomy check result was written to OceanDNA-b33279/tc_result.tsv
[2023-03-16 06:57:52,865] [INFO] ===== Taxonomy check completed =====
[2023-03-16 06:57:52,865] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 06:57:52,865] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg11704a55-b3a7-4261-a1dc-c8602122ce6f/dqc_reference/checkm_data
[2023-03-16 06:57:52,866] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 06:57:53,140] [INFO] Task started: CheckM
[2023-03-16 06:57:53,140] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b33279/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b33279/checkm_input OceanDNA-b33279/checkm_result
[2023-03-16 06:58:31,208] [INFO] Task succeeded: CheckM
[2023-03-16 06:58:31,209] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 60.88%
Contamintation: 8.33%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 06:58:31,211] [INFO] ===== Completeness check finished =====
[2023-03-16 06:58:31,211] [INFO] ===== Start GTDB Search =====
[2023-03-16 06:58:31,211] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b33279/markers.fasta)
[2023-03-16 06:58:31,212] [INFO] Task started: Blastn
[2023-03-16 06:58:31,212] [INFO] Running command: blastn -query OceanDNA-b33279/markers.fasta -db /var/lib/cwl/stg11704a55-b3a7-4261-a1dc-c8602122ce6f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b33279/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 06:58:31,861] [INFO] Task succeeded: Blastn
[2023-03-16 06:58:31,862] [INFO] Selected 10 target genomes.
[2023-03-16 06:58:31,862] [INFO] Target genome list was writen to OceanDNA-b33279/target_genomes_gtdb.txt
[2023-03-16 06:58:31,872] [INFO] Task started: fastANI
[2023-03-16 06:58:31,873] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b3e7142-5627-4e5b-8e44-0cdbfbae621e/OceanDNA-b33279.fa --refList OceanDNA-b33279/target_genomes_gtdb.txt --output OceanDNA-b33279/fastani_result_gtdb.tsv --threads 1
[2023-03-16 06:58:39,287] [INFO] Task succeeded: fastANI
[2023-03-16 06:58:39,294] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 06:58:39,294] [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_009923315.1	s__RFTU01 sp009923315	83.2419	480	620	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__RFTU01	95.0	99.55	99.38	0.93	0.92	4	-
GCA_009925955.1	s__RFTU01 sp009925955	82.201	227	620	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__RFTU01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009918225.1	s__RFTU01 sp009918225	81.8831	290	620	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__RFTU01	95.0	98.76	98.76	0.88	0.88	2	-
GCA_016868355.1	s__RFTU01 sp016868355	80.712	399	620	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__RFTU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008801845.1	s__Ideonella dechloratans	79.4916	278	620	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014873965.1	s__VBDL01 sp014873965	79.431	316	620	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__VBDL01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000969605.1	s__Aquincola tertiaricarbonis	79.3199	324	620	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquincola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302505.1	s__Rubrivivax sp017302505	79.2799	272	620	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rubrivivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012927045.1	s__Azohydromonas caseinilytica	79.2003	311	620	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Azohydromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002198735.1	s__Aquabacterium_A sp002198735	79.073	342	620	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Aquabacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 06:58:39,294] [INFO] GTDB search result was written to OceanDNA-b33279/result_gtdb.tsv
[2023-03-16 06:58:39,294] [INFO] ===== GTDB Search completed =====
[2023-03-16 06:58:39,296] [INFO] DFAST_QC result json was written to OceanDNA-b33279/dqc_result.json
[2023-03-16 06:58:39,296] [INFO] DFAST_QC completed!
[2023-03-16 06:58:39,296] [INFO] Total running time: 0h1m11s