[2023-03-18 09:15:00,477] [INFO] DFAST_QC pipeline started.
[2023-03-18 09:15:00,480] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 09:15:00,481] [INFO] DQC Reference Directory: /var/lib/cwl/stg6f1af227-9a62-455f-a76a-4d4215191ba2/dqc_reference
[2023-03-18 09:15:02,041] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 09:15:02,041] [INFO] Task started: Prodigal
[2023-03-18 09:15:02,041] [INFO] Running command: cat /var/lib/cwl/stg0a8de819-2dc5-4e20-bc88-522e7485d69d/OceanDNA-b29595.fa | prodigal -d OceanDNA-b29595/cds.fna -a OceanDNA-b29595/protein.faa -g 11 -q > /dev/null
[2023-03-18 09:15:19,742] [INFO] Task succeeded: Prodigal
[2023-03-18 09:15:19,742] [INFO] Task started: HMMsearch
[2023-03-18 09:15:19,742] [INFO] Running command: hmmsearch --tblout OceanDNA-b29595/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6f1af227-9a62-455f-a76a-4d4215191ba2/dqc_reference/reference_markers.hmm OceanDNA-b29595/protein.faa > /dev/null
[2023-03-18 09:15:19,936] [INFO] Task succeeded: HMMsearch
[2023-03-18 09:15:19,936] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg0a8de819-2dc5-4e20-bc88-522e7485d69d/OceanDNA-b29595.fa]
[2023-03-18 09:15:19,955] [INFO] Query marker FASTA was written to OceanDNA-b29595/markers.fasta
[2023-03-18 09:15:19,955] [INFO] Task started: Blastn
[2023-03-18 09:15:19,955] [INFO] Running command: blastn -query OceanDNA-b29595/markers.fasta -db /var/lib/cwl/stg6f1af227-9a62-455f-a76a-4d4215191ba2/dqc_reference/reference_markers.fasta -out OceanDNA-b29595/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:15:20,833] [INFO] Task succeeded: Blastn
[2023-03-18 09:15:20,834] [INFO] Selected 20 target genomes.
[2023-03-18 09:15:20,834] [INFO] Target genome list was writen to OceanDNA-b29595/target_genomes.txt
[2023-03-18 09:15:20,845] [INFO] Task started: fastANI
[2023-03-18 09:15:20,845] [INFO] Running command: fastANI --query /var/lib/cwl/stg0a8de819-2dc5-4e20-bc88-522e7485d69d/OceanDNA-b29595.fa --refList OceanDNA-b29595/target_genomes.txt --output OceanDNA-b29595/fastani_result.tsv --threads 1
[2023-03-18 09:15:36,424] [INFO] Task succeeded: fastANI
[2023-03-18 09:15:36,425] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6f1af227-9a62-455f-a76a-4d4215191ba2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 09:15:36,425] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6f1af227-9a62-455f-a76a-4d4215191ba2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 09:15:36,437] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2023-03-18 09:15:36,437] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-18 09:15:36,437] [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
Paracoccus homiensis	strain=DSM 17862	GCA_900111675.1	364199	364199	type	True	97.9562	868	944	95	conclusive
Paracoccus zeaxanthinifaciens	strain=ATCC 21588	GCA_000420145.1	187400	187400	type	True	82.3129	577	944	95	below_threshold
Paracoccus siganidrum	strain=DSM 26381	GCA_003594835.1	1276757	1276757	type	True	81.7164	561	944	95	below_threshold
Paracoccus siganidrum	strain=M26	GCA_003709565.1	1276757	1276757	type	True	81.6379	603	944	95	below_threshold
Paracoccus alcaliphilus	strain=DSM 8512	GCA_900110285.1	34002	34002	type	True	81.3775	554	944	95	below_threshold
Paracoccus salsus	strain=EGI L200073	GCA_021556615.1	2911061	2911061	type	True	81.3425	562	944	95	below_threshold
Paracoccus indicus	strain=IO390502	GCA_003056335.1	2079229	2079229	type	True	81.3182	567	944	95	below_threshold
Paracoccus aestuarii	strain=DSM 19484	GCA_003594815.1	453842	453842	type	True	81.2412	529	944	95	below_threshold
Paracoccus shandongensis	strain=wg2	GCA_017315735.1	2816048	2816048	type	True	81.2041	542	944	95	below_threshold
Paracoccus sediminilitoris	strain=DSL-16	GCA_003259195.1	2202419	2202419	type	True	81.1638	561	944	95	below_threshold
Paracoccus hibiscisoli	strain=CCTCC AB2016182	GCA_005048265.1	2023261	2023261	type	True	80.9432	584	944	95	below_threshold
Paracoccus aerius	strain=KCTC 42845	GCA_014656455.1	1915382	1915382	type	True	80.9203	554	944	95	below_threshold
Paracoccus caeni	strain=MJ17	GCA_016629665.1	657651	657651	type	True	80.8157	542	944	95	below_threshold
Paracoccus seriniphilus	strain=DSM 14827	GCA_900199195.1	184748	184748	type	True	80.7933	543	944	95	below_threshold
Paracoccus everestensis	strain=S8-55	GCA_021491915.1	2903900	2903900	type	True	80.6859	516	944	95	below_threshold
Paracoccus bogoriensis	strain=BOG6	GCA_019431455.1	242065	242065	type	True	80.5567	511	944	95	below_threshold
Paracoccus amoyensis	strain=11-3	GCA_014490725.1	2760093	2760093	type	True	79.9268	479	944	95	below_threshold
Paracoccus limosus	strain=JCM 17370	GCA_009711185.1	913252	913252	type	True	79.8813	464	944	95	below_threshold
Paracoccus tegillarcae	strain=BM15	GCA_002847305.1	1529068	1529068	type	True	79.7791	491	944	95	below_threshold
Paracoccus onubensis	strain=1011MAR3C25	GCA_003591515.1	1675788	1675788	type	True	79.397	475	944	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 09:15:36,438] [INFO] DFAST Taxonomy check result was written to OceanDNA-b29595/tc_result.tsv
[2023-03-18 09:15:36,438] [INFO] ===== Taxonomy check completed =====
[2023-03-18 09:15:36,438] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 09:15:36,438] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6f1af227-9a62-455f-a76a-4d4215191ba2/dqc_reference/checkm_data
[2023-03-18 09:15:36,439] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 09:15:36,443] [INFO] Task started: CheckM
[2023-03-18 09:15:36,443] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b29595/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b29595/checkm_input OceanDNA-b29595/checkm_result
[2023-03-18 09:16:24,073] [INFO] Task succeeded: CheckM
[2023-03-18 09:16:24,073] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.74%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 09:16:24,076] [INFO] ===== Completeness check finished =====
[2023-03-18 09:16:24,076] [INFO] ===== Start GTDB Search =====
[2023-03-18 09:16:24,076] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b29595/markers.fasta)
[2023-03-18 09:16:24,077] [INFO] Task started: Blastn
[2023-03-18 09:16:24,077] [INFO] Running command: blastn -query OceanDNA-b29595/markers.fasta -db /var/lib/cwl/stg6f1af227-9a62-455f-a76a-4d4215191ba2/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b29595/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:16:25,703] [INFO] Task succeeded: Blastn
[2023-03-18 09:16:25,703] [INFO] Selected 13 target genomes.
[2023-03-18 09:16:25,704] [INFO] Target genome list was writen to OceanDNA-b29595/target_genomes_gtdb.txt
[2023-03-18 09:16:25,717] [INFO] Task started: fastANI
[2023-03-18 09:16:25,718] [INFO] Running command: fastANI --query /var/lib/cwl/stg0a8de819-2dc5-4e20-bc88-522e7485d69d/OceanDNA-b29595.fa --refList OceanDNA-b29595/target_genomes_gtdb.txt --output OceanDNA-b29595/fastani_result_gtdb.tsv --threads 1
[2023-03-18 09:16:35,753] [INFO] Task succeeded: fastANI
[2023-03-18 09:16:35,762] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 09:16:35,762] [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_900111675.1	s__Paracoccus homiensis	97.9562	868	944	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000420145.1	s__Paracoccus zeaxanthinifaciens	82.3037	578	944	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017744015.1	s__Paracoccus sp002732665	82.2921	598	944	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.29	98.58	0.98	0.95	3	-
GCF_018860165.1	s__Paracoccus sp018860165	82.0112	605	944	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860625.1	s__Paracoccus sp018860625	81.8908	570	944	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003709565.1	s__Paracoccus siganidrum	81.64	603	944	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.99	99.99	0.98	0.98	2	-
GCA_002294185.1	s__Paracoccus sp002294185	81.4954	560	944	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	99.77	99.74	0.93	0.89	5	-
GCF_900110285.1	s__Paracoccus alcaliphilus	81.3901	553	944	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003056335.1	s__Paracoccus indicus	81.3182	567	944	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003594815.1	s__Paracoccus aestuarii	81.2535	529	944	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259195.1	s__Paracoccus sediminilitoris	81.1518	562	944	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	95.17	95.17	0.89	0.89	2	-
GCF_005048265.1	s__Paracoccus hibiscisoli	80.9432	584	944	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	96.40	96.40	0.91	0.91	2	-
GCF_016629665.1	s__Paracoccus caeni	80.8273	541	944	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Paracoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 09:16:35,762] [INFO] GTDB search result was written to OceanDNA-b29595/result_gtdb.tsv
[2023-03-18 09:16:35,762] [INFO] ===== GTDB Search completed =====
[2023-03-18 09:16:35,764] [INFO] DFAST_QC result json was written to OceanDNA-b29595/dqc_result.json
[2023-03-18 09:16:35,764] [INFO] DFAST_QC completed!
[2023-03-18 09:16:35,764] [INFO] Total running time: 0h1m35s