[2023-03-17 02:49:37,529] [INFO] DFAST_QC pipeline started.
[2023-03-17 02:49:37,529] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 02:49:37,529] [INFO] DQC Reference Directory: /var/lib/cwl/stg049d52de-5f7a-4d76-a033-ba61e9e55b8d/dqc_reference
[2023-03-17 02:49:38,766] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 02:49:38,767] [INFO] Task started: Prodigal
[2023-03-17 02:49:38,767] [INFO] Running command: cat /var/lib/cwl/stg4ea2cb2f-7474-4dce-945f-72c7b1e7c552/OceanDNA-b9787.fa | prodigal -d OceanDNA-b9787/cds.fna -a OceanDNA-b9787/protein.faa -g 11 -q > /dev/null
[2023-03-17 02:50:06,318] [INFO] Task succeeded: Prodigal
[2023-03-17 02:50:06,319] [INFO] Task started: HMMsearch
[2023-03-17 02:50:06,319] [INFO] Running command: hmmsearch --tblout OceanDNA-b9787/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg049d52de-5f7a-4d76-a033-ba61e9e55b8d/dqc_reference/reference_markers.hmm OceanDNA-b9787/protein.faa > /dev/null
[2023-03-17 02:50:06,542] [INFO] Task succeeded: HMMsearch
[2023-03-17 02:50:06,543] [INFO] Found 6/6 markers.
[2023-03-17 02:50:06,564] [INFO] Query marker FASTA was written to OceanDNA-b9787/markers.fasta
[2023-03-17 02:50:06,564] [INFO] Task started: Blastn
[2023-03-17 02:50:06,564] [INFO] Running command: blastn -query OceanDNA-b9787/markers.fasta -db /var/lib/cwl/stg049d52de-5f7a-4d76-a033-ba61e9e55b8d/dqc_reference/reference_markers.fasta -out OceanDNA-b9787/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:50:07,129] [INFO] Task succeeded: Blastn
[2023-03-17 02:50:07,130] [INFO] Selected 26 target genomes.
[2023-03-17 02:50:07,130] [INFO] Target genome list was writen to OceanDNA-b9787/target_genomes.txt
[2023-03-17 02:50:07,281] [INFO] Task started: fastANI
[2023-03-17 02:50:07,281] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ea2cb2f-7474-4dce-945f-72c7b1e7c552/OceanDNA-b9787.fa --refList OceanDNA-b9787/target_genomes.txt --output OceanDNA-b9787/fastani_result.tsv --threads 1
[2023-03-17 02:50:23,522] [INFO] Task succeeded: fastANI
[2023-03-17 02:50:23,523] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg049d52de-5f7a-4d76-a033-ba61e9e55b8d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 02:50:23,523] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg049d52de-5f7a-4d76-a033-ba61e9e55b8d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 02:50:23,535] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2023-03-17 02:50:23,535] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-17 02:50:23,535] [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
Muricauda lutaonensis	strain=CC-HSB-11	GCA_000963865.1	516051	516051	type	True	97.7648	891	1053	95	conclusive
Muricauda pacifica	strain=DSM 25027	GCA_003001695.1	1080225	1080225	type	True	77.2727	122	1053	95	below_threshold
Muricauda antarctica	strain=DSM 26351	GCA_900112295.1	1055723	1055723	type	True	76.9443	158	1053	95	below_threshold
Muricauda oceani	strain=501str8	GCA_011068285.1	2698672	2698672	type	True	76.9262	142	1053	95	below_threshold
Muricauda oceani	strain=501str8	GCA_019457985.1	2698672	2698672	type	True	76.9217	141	1053	95	below_threshold
Muricauda antarctica	strain=CGMCC 1.12174	GCA_900142405.1	1055723	1055723	type	True	76.8831	158	1053	95	below_threshold
Muricauda nanhaiensis	strain=SM1704	GCA_003382275.1	2292706	2292706	type	True	76.8534	139	1053	95	below_threshold
Maribacter flavus	strain=KCTC 42508	GCA_008386635.1	1658664	1658664	type	True	76.8509	75	1053	95	below_threshold
Muricauda beolgyonensis	strain=KCTC 23501	GCA_003992615.1	864064	864064	type	True	76.8205	164	1053	95	below_threshold
Muricauda taeanensis	strain=JCM 17757	GCA_003584105.1	1005926	1005926	type	True	76.7847	160	1053	95	below_threshold
Muricauda alvinocaridis	strain=SCR12	GCA_004916895.1	2530200	2530200	type	True	76.7569	159	1053	95	below_threshold
Muricauda aequoris	strain=NH166	GCA_003584165.1	2306997	2306997	type	True	76.7098	175	1053	95	below_threshold
Muricauda aequoris	strain=NH166	GCA_008017345.1	2306997	2306997	type	True	76.7098	175	1053	95	below_threshold
Muricauda maritima	strain=72	GCA_008017365.1	2306998	2306998	type	True	76.6522	178	1053	95	below_threshold
Muricauda maritima	strain=72	GCA_003584135.1	2306998	2306998	type	True	76.6522	178	1053	95	below_threshold
Muricauda chongwuensis	strain=HICW	GCA_013376415.1	2697365	2697365	type	True	76.5527	139	1053	95	below_threshold
Muricauda hadalis	strain=MT-229	GCA_007785775.2	2597517	2597517	type	True	76.5411	180	1053	95	below_threshold
Muricauda aurea	strain=BC31-1-A7	GCA_017313785.1	2915619	2915619	type	True	76.3179	125	1053	95	below_threshold
Maribacter polysiphoniae	strain=DSM 23514	GCA_003148665.1	429344	429344	type	True	76.2589	83	1053	95	below_threshold
Pricia antarctica	strain=DSM 23421	GCA_900101815.1	641691	641691	type	True	75.7182	78	1053	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 02:50:23,536] [INFO] DFAST Taxonomy check result was written to OceanDNA-b9787/tc_result.tsv
[2023-03-17 02:50:23,537] [INFO] ===== Taxonomy check completed =====
[2023-03-17 02:50:23,538] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 02:50:23,538] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg049d52de-5f7a-4d76-a033-ba61e9e55b8d/dqc_reference/checkm_data
[2023-03-17 02:50:23,538] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 02:50:23,545] [INFO] Task started: CheckM
[2023-03-17 02:50:23,545] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b9787/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b9787/checkm_input OceanDNA-b9787/checkm_result
[2023-03-17 02:51:32,477] [INFO] Task succeeded: CheckM
[2023-03-17 02:51:32,478] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.39%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 02:51:32,560] [INFO] ===== Completeness check finished =====
[2023-03-17 02:51:32,560] [INFO] ===== Start GTDB Search =====
[2023-03-17 02:51:32,560] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b9787/markers.fasta)
[2023-03-17 02:51:32,561] [INFO] Task started: Blastn
[2023-03-17 02:51:32,561] [INFO] Running command: blastn -query OceanDNA-b9787/markers.fasta -db /var/lib/cwl/stg049d52de-5f7a-4d76-a033-ba61e9e55b8d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b9787/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 02:51:33,318] [INFO] Task succeeded: Blastn
[2023-03-17 02:51:33,324] [INFO] Selected 25 target genomes.
[2023-03-17 02:51:33,325] [INFO] Target genome list was writen to OceanDNA-b9787/target_genomes_gtdb.txt
[2023-03-17 02:51:33,431] [INFO] Task started: fastANI
[2023-03-17 02:51:33,431] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ea2cb2f-7474-4dce-945f-72c7b1e7c552/OceanDNA-b9787.fa --refList OceanDNA-b9787/target_genomes_gtdb.txt --output OceanDNA-b9787/fastani_result_gtdb.tsv --threads 1
[2023-03-17 02:51:50,061] [INFO] Task succeeded: fastANI
[2023-03-17 02:51:50,074] [INFO] Found 24 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 02:51:50,074] [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
GCF_000963865.1	s__Muricauda_A lutaonensis	97.7648	891	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda_A	95.0	97.74	97.69	0.86	0.85	5	conclusive
GCA_002699205.1	s__Muricauda sp002699205	81.1662	148	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	99.91	99.91	0.89	0.89	2	-
GCF_017313275.1	s__Muricauda lutimaris_A	77.6922	148	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003712125.1	s__Muricauda_A sp003712125	77.0478	159	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011068285.1	s__Muricauda sp011068285	76.9433	141	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008386635.1	s__Maribacter flavus	76.8509	75	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	96.59	96.59	0.88	0.88	2	-
GCF_003992615.1	s__Muricauda beolgyonensis	76.8208	163	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013214065.1	s__DT-32 sp013214065	76.8124	149	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__DT-32	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003584105.1	s__Muricauda taeanensis	76.7847	160	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	97.68	97.68	0.85	0.85	3	-
GCF_004916895.1	s__Muricauda alvinocaridis	76.7569	159	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003584165.1	s__Muricauda sp003584165	76.7224	174	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000745185.1	s__Muricauda sp000745185	76.7117	176	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013911645.1	s__Muricauda sp013911645	76.7014	140	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141855.1	s__Pseudozobellia thermophila	76.6903	105	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pseudozobellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003584135.1	s__Muricauda sp003584135	76.6643	177	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000224085.1	s__Muricauda ruestringensis	76.6153	139	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003385855.1	s__Muricauda sp003385855	76.5728	170	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	97.98	97.98	0.89	0.89	2	-
GCF_007785775.2	s__Muricauda sp003973595	76.5411	180	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	98.36	98.36	0.87	0.87	2	-
GCF_017313105.1	s__Muricauda sp017313105	76.5333	130	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010468565.1	s__Muricauda sp010468565	76.2983	143	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003148665.1	s__Maribacter_A polysiphoniae	76.2589	83	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_A	95.0	99.27	98.55	0.95	0.91	3	-
GCF_003626755.1	s__Ulvibacterium marinum	76.1876	110	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ulvibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000973105.1	s__Zobellia galactanivorans	76.0626	99	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	99.09	99.05	0.92	0.91	3	-
GCF_014596745.1	s__Maribacter_A sp014596745	76.0428	81	1053	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 02:51:50,077] [INFO] GTDB search result was written to OceanDNA-b9787/result_gtdb.tsv
[2023-03-17 02:51:50,077] [INFO] ===== GTDB Search completed =====
[2023-03-17 02:51:50,082] [INFO] DFAST_QC result json was written to OceanDNA-b9787/dqc_result.json
[2023-03-17 02:51:50,083] [INFO] DFAST_QC completed!
[2023-03-17 02:51:50,083] [INFO] Total running time: 0h2m13s