[2023-03-15 05:00:03,547] [INFO] DFAST_QC pipeline started.
[2023-03-15 05:00:03,547] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 05:00:03,547] [INFO] DQC Reference Directory: /var/lib/cwl/stgd77dde9a-c873-4310-b8df-f18dc5a810bd/dqc_reference
[2023-03-15 05:00:09,723] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 05:00:09,724] [INFO] Task started: Prodigal
[2023-03-15 05:00:09,724] [INFO] Running command: cat /var/lib/cwl/stg5fb3d7aa-ba05-4db2-9c0a-e8852aa5b170/OceanDNA-b22760.fa | prodigal -d OceanDNA-b22760/cds.fna -a OceanDNA-b22760/protein.faa -g 11 -q > /dev/null
[2023-03-15 05:00:29,405] [INFO] Task succeeded: Prodigal
[2023-03-15 05:00:29,406] [INFO] Task started: HMMsearch
[2023-03-15 05:00:29,406] [INFO] Running command: hmmsearch --tblout OceanDNA-b22760/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd77dde9a-c873-4310-b8df-f18dc5a810bd/dqc_reference/reference_markers.hmm OceanDNA-b22760/protein.faa > /dev/null
[2023-03-15 05:00:29,684] [INFO] Task succeeded: HMMsearch
[2023-03-15 05:00:29,685] [INFO] Found 6/6 markers.
[2023-03-15 05:00:29,717] [INFO] Query marker FASTA was written to OceanDNA-b22760/markers.fasta
[2023-03-15 05:00:29,718] [INFO] Task started: Blastn
[2023-03-15 05:00:29,718] [INFO] Running command: blastn -query OceanDNA-b22760/markers.fasta -db /var/lib/cwl/stgd77dde9a-c873-4310-b8df-f18dc5a810bd/dqc_reference/reference_markers.fasta -out OceanDNA-b22760/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:00:33,631] [INFO] Task succeeded: Blastn
[2023-03-15 05:00:33,632] [INFO] Selected 25 target genomes.
[2023-03-15 05:00:33,633] [INFO] Target genome list was writen to OceanDNA-b22760/target_genomes.txt
[2023-03-15 05:00:33,646] [INFO] Task started: fastANI
[2023-03-15 05:00:33,646] [INFO] Running command: fastANI --query /var/lib/cwl/stg5fb3d7aa-ba05-4db2-9c0a-e8852aa5b170/OceanDNA-b22760.fa --refList OceanDNA-b22760/target_genomes.txt --output OceanDNA-b22760/fastani_result.tsv --threads 1
[2023-03-15 05:01:00,507] [INFO] Task succeeded: fastANI
[2023-03-15 05:01:00,508] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd77dde9a-c873-4310-b8df-f18dc5a810bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 05:01:00,508] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd77dde9a-c873-4310-b8df-f18dc5a810bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 05:01:00,515] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 05:01:00,515] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 05:01:00,515] [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
Pseudobythopirellula maris	strain=Mal64	GCA_007859945.1	2527991	2527991	type	True	76.5735	70	987	95	below_threshold
Posidoniimonas polymericola	strain=Pla123a	GCA_007859935.1	2528002	2528002	type	True	76.2419	88	987	95	below_threshold
Lacipirellula parvula	strain=PX69	GCA_009177095.1	2650471	2650471	type	True	76.0885	66	987	95	below_threshold
Posidoniimonas corsicana	strain=KOR34	GCA_007859765.1	1938618	1938618	type	True	76.0152	91	987	95	below_threshold
Lacipirellula limnantheis	strain=I41	GCA_007746075.1	2528024	2528024	type	True	75.7336	62	987	95	below_threshold
Aquisphaera giovannonii	strain=OJF2	GCA_008087625.1	406548	406548	type	True	75.4589	95	987	95	below_threshold
Paludisphaera borealis	strain=PX4	GCA_001956985.1	1387353	1387353	type	True	75.424	74	987	95	below_threshold
Tautonia plasticadhaerens	strain=ElP	GCA_007752535.1	2527974	2527974	type	True	75.2812	76	987	95	below_threshold
Tautonia sociabilis	strain=GM2012	GCA_003977685.1	2080755	2080755	type	True	75.1818	74	987	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 05:01:00,516] [INFO] DFAST Taxonomy check result was written to OceanDNA-b22760/tc_result.tsv
[2023-03-15 05:01:00,517] [INFO] ===== Taxonomy check completed =====
[2023-03-15 05:01:00,517] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 05:01:00,517] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd77dde9a-c873-4310-b8df-f18dc5a810bd/dqc_reference/checkm_data
[2023-03-15 05:01:00,517] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 05:01:00,531] [INFO] Task started: CheckM
[2023-03-15 05:01:00,532] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b22760/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b22760/checkm_input OceanDNA-b22760/checkm_result
[2023-03-15 05:01:53,772] [INFO] Task succeeded: CheckM
[2023-03-15 05:01:53,773] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.08%
Contamintation: 0.84%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-03-15 05:01:53,777] [INFO] ===== Completeness check finished =====
[2023-03-15 05:01:53,778] [INFO] ===== Start GTDB Search =====
[2023-03-15 05:01:53,778] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b22760/markers.fasta)
[2023-03-15 05:01:53,779] [INFO] Task started: Blastn
[2023-03-15 05:01:53,779] [INFO] Running command: blastn -query OceanDNA-b22760/markers.fasta -db /var/lib/cwl/stgd77dde9a-c873-4310-b8df-f18dc5a810bd/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b22760/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 05:01:54,561] [INFO] Task succeeded: Blastn
[2023-03-15 05:01:54,562] [INFO] Selected 16 target genomes.
[2023-03-15 05:01:54,562] [INFO] Target genome list was writen to OceanDNA-b22760/target_genomes_gtdb.txt
[2023-03-15 05:01:54,662] [INFO] Task started: fastANI
[2023-03-15 05:01:54,662] [INFO] Running command: fastANI --query /var/lib/cwl/stg5fb3d7aa-ba05-4db2-9c0a-e8852aa5b170/OceanDNA-b22760.fa --refList OceanDNA-b22760/target_genomes_gtdb.txt --output OceanDNA-b22760/fastani_result_gtdb.tsv --threads 1
[2023-03-15 05:02:05,960] [INFO] Task succeeded: fastANI
[2023-03-15 05:02:05,968] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 05:02:05,969] [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_018401745.1	s__M30B53 sp018401745	90.6245	584	987	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__M30B53	95.0	96.02	95.94	0.68	0.66	3	-
GCA_016779265.1	s__M30B53 sp016779265	80.3371	534	987	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__M30B53	95.0	99.26	99.20	0.88	0.86	5	-
GCA_903919035.1	s__QWPN01 sp903919035	77.9692	175	987	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	99.57	99.56	0.90	0.89	5	-
GCA_016872925.1	s__QWPN01 sp016872925	77.8489	243	987	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	77.8098	180	987	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016872955.1	s__QWPN01 sp016872955	77.5737	160	987	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903831155.1	s__QWPN01 sp903831155	77.3904	243	987	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014192425.1	s__QWPN01 sp014192425	77.3884	213	987	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903958265.1	s__QWPN01 sp903958265	77.3602	161	987	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	98.26	98.26	0.80	0.80	2	-
GCA_003670825.1	s__QWPN01 sp003670825	77.2857	131	987	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016872555.1	s__F1-20-MAGs016 sp016872555	77.1973	241	987	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_017853835.1	s__QWPN01 sp017853835	77.1796	178	987	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__QWPN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_010027105.1	s__RGVT01 sp010027105	77.1743	166	987	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__UBA1268;g__RGVT01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 05:02:05,971] [INFO] GTDB search result was written to OceanDNA-b22760/result_gtdb.tsv
[2023-03-15 05:02:05,971] [INFO] ===== GTDB Search completed =====
[2023-03-15 05:02:05,974] [INFO] DFAST_QC result json was written to OceanDNA-b22760/dqc_result.json
[2023-03-15 05:02:05,974] [INFO] DFAST_QC completed!
[2023-03-15 05:02:05,974] [INFO] Total running time: 0h2m2s