[2023-03-18 01:37:06,010] [INFO] DFAST_QC pipeline started.
[2023-03-18 01:37:06,010] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 01:37:06,010] [INFO] DQC Reference Directory: /var/lib/cwl/stg46b9b24e-5f69-4069-b6e9-94c38b65d4fb/dqc_reference
[2023-03-18 01:37:07,102] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 01:37:07,103] [INFO] Task started: Prodigal
[2023-03-18 01:37:07,103] [INFO] Running command: cat /var/lib/cwl/stg7b550df3-fdb9-4bca-8f90-0685b3ab1366/OceanDNA-b45807.fa | prodigal -d OceanDNA-b45807/cds.fna -a OceanDNA-b45807/protein.faa -g 11 -q > /dev/null
[2023-03-18 01:37:47,275] [INFO] Task succeeded: Prodigal
[2023-03-18 01:37:47,276] [INFO] Task started: HMMsearch
[2023-03-18 01:37:47,276] [INFO] Running command: hmmsearch --tblout OceanDNA-b45807/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg46b9b24e-5f69-4069-b6e9-94c38b65d4fb/dqc_reference/reference_markers.hmm OceanDNA-b45807/protein.faa > /dev/null
[2023-03-18 01:37:47,498] [INFO] Task succeeded: HMMsearch
[2023-03-18 01:37:47,499] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg7b550df3-fdb9-4bca-8f90-0685b3ab1366/OceanDNA-b45807.fa]
[2023-03-18 01:37:47,546] [INFO] Query marker FASTA was written to OceanDNA-b45807/markers.fasta
[2023-03-18 01:37:47,547] [INFO] Task started: Blastn
[2023-03-18 01:37:47,547] [INFO] Running command: blastn -query OceanDNA-b45807/markers.fasta -db /var/lib/cwl/stg46b9b24e-5f69-4069-b6e9-94c38b65d4fb/dqc_reference/reference_markers.fasta -out OceanDNA-b45807/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:37:48,126] [INFO] Task succeeded: Blastn
[2023-03-18 01:37:48,139] [INFO] Selected 12 target genomes.
[2023-03-18 01:37:48,139] [INFO] Target genome list was writen to OceanDNA-b45807/target_genomes.txt
[2023-03-18 01:37:48,147] [INFO] Task started: fastANI
[2023-03-18 01:37:48,147] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b550df3-fdb9-4bca-8f90-0685b3ab1366/OceanDNA-b45807.fa --refList OceanDNA-b45807/target_genomes.txt --output OceanDNA-b45807/fastani_result.tsv --threads 1
[2023-03-18 01:37:56,535] [INFO] Task succeeded: fastANI
[2023-03-18 01:37:56,535] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg46b9b24e-5f69-4069-b6e9-94c38b65d4fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 01:37:56,535] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg46b9b24e-5f69-4069-b6e9-94c38b65d4fb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 01:37:56,540] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 01:37:56,540] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 01:37:56,540] [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
Rariglobus hedericola	strain=53C-WASEF	GCA_007559335.1	2597822	2597822	type	True	76.5347	73	1351	95	below_threshold
Nibricoccus aquaticus	strain=HZ-65	GCA_002310495.1	2576891	2576891	type	True	76.5138	82	1351	95	below_threshold
Ereboglobus luteus	strain=Ho45	GCA_003096195.1	1796921	1796921	type	True	76.0644	51	1351	95	below_threshold
Geminisphaera colitermitum	strain=TAV2	GCA_000171235.2	1148786	1148786	type	True	75.9495	71	1351	95	below_threshold
Opitutus terrae	strain=PB90-1	GCA_000019965.1	107709	107709	type	True	75.9051	69	1351	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 01:37:56,543] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45807/tc_result.tsv
[2023-03-18 01:37:56,545] [INFO] ===== Taxonomy check completed =====
[2023-03-18 01:37:56,545] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 01:37:56,545] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg46b9b24e-5f69-4069-b6e9-94c38b65d4fb/dqc_reference/checkm_data
[2023-03-18 01:37:56,546] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 01:37:56,566] [INFO] Task started: CheckM
[2023-03-18 01:37:56,566] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45807/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45807/checkm_input OceanDNA-b45807/checkm_result
[2023-03-18 01:39:33,647] [INFO] Task succeeded: CheckM
[2023-03-18 01:39:33,648] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 01:39:33,653] [INFO] ===== Completeness check finished =====
[2023-03-18 01:39:33,653] [INFO] ===== Start GTDB Search =====
[2023-03-18 01:39:33,654] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45807/markers.fasta)
[2023-03-18 01:39:33,655] [INFO] Task started: Blastn
[2023-03-18 01:39:33,655] [INFO] Running command: blastn -query OceanDNA-b45807/markers.fasta -db /var/lib/cwl/stg46b9b24e-5f69-4069-b6e9-94c38b65d4fb/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45807/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 01:39:34,754] [INFO] Task succeeded: Blastn
[2023-03-18 01:39:34,762] [INFO] Selected 23 target genomes.
[2023-03-18 01:39:34,762] [INFO] Target genome list was writen to OceanDNA-b45807/target_genomes_gtdb.txt
[2023-03-18 01:39:34,785] [INFO] Task started: fastANI
[2023-03-18 01:39:34,785] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b550df3-fdb9-4bca-8f90-0685b3ab1366/OceanDNA-b45807.fa --refList OceanDNA-b45807/target_genomes_gtdb.txt --output OceanDNA-b45807/fastani_result_gtdb.tsv --threads 1
[2023-03-18 01:39:51,561] [INFO] Task succeeded: fastANI
[2023-03-18 01:39:51,570] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 01:39:51,571] [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_018667915.1	s__M30B9 sp018667915	76.949	167	1351	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__M30B9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018402455.1	s__M30B9 sp018402455	76.7194	152	1351	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__M30B9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903938935.1	s__Tous-C4FEB sp903938935	76.7018	61	1351	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Tous-C4FEB	95.0	98.58	98.56	0.78	0.76	6	-
GCA_000972765.1	s__IMCC26134_A sp000972765	76.6961	74	1351	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__IMCC26134_A	95.0	99.41	99.35	0.95	0.94	9	-
GCA_903876795.1	s__Rariglobus sp903876795	76.6552	75	1351	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Rariglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018239845.1	s__Opitutus sp018239845	76.5799	87	1351	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opitutus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007559335.1	s__Rariglobus hedericola	76.5639	72	1351	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Rariglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002310495.1	s__Nibricoccus aquaticus	76.5138	82	1351	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Nibricoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016795565.1	s__Lacunisphaera sp016795565	76.4544	53	1351	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Lacunisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903877135.1	s__Opitutus sp903877135	76.333	61	1351	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opitutus	95.0	99.97	99.95	0.97	0.97	4	-
GCA_903820035.1	s__ER46 sp903820035	76.301	67	1351	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	99.61	99.58	0.90	0.89	3	-
GCA_002288455.1	s__ER46 sp002288455	76.1959	78	1351	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104925.1	s__Lacunisphaera sp900104925	76.1122	61	1351	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Lacunisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000171235.2	s__Geminisphaera colitermitum	75.9495	71	1351	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Geminisphaera	95.0	97.34	97.31	0.79	0.79	3	-
GCA_016217595.1	s__MWDT01 sp016217595	75.9341	54	1351	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__MWDT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003054665.1	s__EW11 sp003054665	75.9034	58	1351	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__EW11	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 01:39:51,571] [INFO] GTDB search result was written to OceanDNA-b45807/result_gtdb.tsv
[2023-03-18 01:39:51,571] [INFO] ===== GTDB Search completed =====
[2023-03-18 01:39:51,572] [INFO] DFAST_QC result json was written to OceanDNA-b45807/dqc_result.json
[2023-03-18 01:39:51,572] [INFO] DFAST_QC completed!
[2023-03-18 01:39:51,572] [INFO] Total running time: 0h2m46s