[2023-03-18 07:29:30,341] [INFO] DFAST_QC pipeline started.
[2023-03-18 07:29:30,341] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 07:29:30,341] [INFO] DQC Reference Directory: /var/lib/cwl/stg53b7808e-41de-43fa-b403-c8f4885328e1/dqc_reference
[2023-03-18 07:29:31,935] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 07:29:31,935] [INFO] Task started: Prodigal
[2023-03-18 07:29:31,935] [INFO] Running command: cat /var/lib/cwl/stg2a4f9933-bf0c-4ded-89e2-3f8cf8495182/OceanDNA-b29548.fa | prodigal -d OceanDNA-b29548/cds.fna -a OceanDNA-b29548/protein.faa -g 11 -q > /dev/null
[2023-03-18 07:29:43,819] [INFO] Task succeeded: Prodigal
[2023-03-18 07:29:43,820] [INFO] Task started: HMMsearch
[2023-03-18 07:29:43,820] [INFO] Running command: hmmsearch --tblout OceanDNA-b29548/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg53b7808e-41de-43fa-b403-c8f4885328e1/dqc_reference/reference_markers.hmm OceanDNA-b29548/protein.faa > /dev/null
[2023-03-18 07:29:44,003] [INFO] Task succeeded: HMMsearch
[2023-03-18 07:29:44,003] [INFO] Found 6/6 markers.
[2023-03-18 07:29:44,020] [INFO] Query marker FASTA was written to OceanDNA-b29548/markers.fasta
[2023-03-18 07:29:44,020] [INFO] Task started: Blastn
[2023-03-18 07:29:44,020] [INFO] Running command: blastn -query OceanDNA-b29548/markers.fasta -db /var/lib/cwl/stg53b7808e-41de-43fa-b403-c8f4885328e1/dqc_reference/reference_markers.fasta -out OceanDNA-b29548/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:29:44,664] [INFO] Task succeeded: Blastn
[2023-03-18 07:29:44,665] [INFO] Selected 19 target genomes.
[2023-03-18 07:29:44,665] [INFO] Target genome list was writen to OceanDNA-b29548/target_genomes.txt
[2023-03-18 07:29:44,675] [INFO] Task started: fastANI
[2023-03-18 07:29:44,675] [INFO] Running command: fastANI --query /var/lib/cwl/stg2a4f9933-bf0c-4ded-89e2-3f8cf8495182/OceanDNA-b29548.fa --refList OceanDNA-b29548/target_genomes.txt --output OceanDNA-b29548/fastani_result.tsv --threads 1
[2023-03-18 07:29:56,149] [INFO] Task succeeded: fastANI
[2023-03-18 07:29:56,149] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg53b7808e-41de-43fa-b403-c8f4885328e1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 07:29:56,149] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg53b7808e-41de-43fa-b403-c8f4885328e1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 07:29:56,158] [INFO] Found 12 fastANI hits (3 hits with ANI > threshold)
[2023-03-18 07:29:56,158] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-18 07:29:56,158] [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
Nereida ignava	strain=DSM 16309	GCA_900114125.1	282199	282199	type	True	99.6188	557	598	95	conclusive
Nereida ignava	strain=CECT 5292	GCA_001049735.1	282199	282199	type	True	99.6007	561	598	95	conclusive
Nereida ignava	strain=CECT 5292	GCA_001404155.1	282199	282199	type	True	99.6007	561	598	95	conclusive
Yoonia maritima	strain=DSM 101533	GCA_003003285.1	1435347	1435347	type	True	76.7569	73	598	95	below_threshold
Sulfitobacter sediminilitoris	strain=JBTF-M27	GCA_010667575.1	2698830	2698830	type	True	76.5917	52	598	95	below_threshold
Yoonia tamlensis	strain=DSM 26879	GCA_900115105.1	390270	390270	type	True	76.4269	76	598	95	below_threshold
Sulfitobacter geojensis	strain=DSM 101063	GCA_013407805.1	1342299	1342299	type	True	76.3612	58	598	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	76.3252	63	598	95	below_threshold
Thalassobius autumnalis	strain=CECT 5118	GCA_001458255.1	2072972	2072972	type	True	76.1745	66	598	95	below_threshold
Thalassobacter stenotrophicus	strain=CECT 5294	GCA_001458315.1	266809	266809	type	True	76.1738	75	598	95	below_threshold
Thalassobacter stenotrophicus	strain=DSM 16310	GCA_900141945.1	266809	266809	type	True	76.1738	75	598	95	below_threshold
Pseudoprimorskyibacter insulae	strain=CECT 8871	GCA_900302505.1	1695997	1695997	type	True	76.11	57	598	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 07:29:56,158] [INFO] DFAST Taxonomy check result was written to OceanDNA-b29548/tc_result.tsv
[2023-03-18 07:29:56,158] [INFO] ===== Taxonomy check completed =====
[2023-03-18 07:29:56,158] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 07:29:56,158] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg53b7808e-41de-43fa-b403-c8f4885328e1/dqc_reference/checkm_data
[2023-03-18 07:29:56,159] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 07:29:56,163] [INFO] Task started: CheckM
[2023-03-18 07:29:56,163] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b29548/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b29548/checkm_input OceanDNA-b29548/checkm_result
[2023-03-18 07:30:30,160] [INFO] Task succeeded: CheckM
[2023-03-18 07:30:30,161] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 07:30:30,163] [INFO] ===== Completeness check finished =====
[2023-03-18 07:30:30,163] [INFO] ===== Start GTDB Search =====
[2023-03-18 07:30:30,163] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b29548/markers.fasta)
[2023-03-18 07:30:30,163] [INFO] Task started: Blastn
[2023-03-18 07:30:30,163] [INFO] Running command: blastn -query OceanDNA-b29548/markers.fasta -db /var/lib/cwl/stg53b7808e-41de-43fa-b403-c8f4885328e1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b29548/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:30:31,279] [INFO] Task succeeded: Blastn
[2023-03-18 07:30:31,280] [INFO] Selected 27 target genomes.
[2023-03-18 07:30:31,280] [INFO] Target genome list was writen to OceanDNA-b29548/target_genomes_gtdb.txt
[2023-03-18 07:30:31,409] [INFO] Task started: fastANI
[2023-03-18 07:30:31,409] [INFO] Running command: fastANI --query /var/lib/cwl/stg2a4f9933-bf0c-4ded-89e2-3f8cf8495182/OceanDNA-b29548.fa --refList OceanDNA-b29548/target_genomes_gtdb.txt --output OceanDNA-b29548/fastani_result_gtdb.tsv --threads 1
[2023-03-18 07:30:47,151] [INFO] Task succeeded: fastANI
[2023-03-18 07:30:47,161] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 07:30:47,162] [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_001049735.1	s__Nereida ignava	99.6007	561	598	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Nereida	95.0	99.99	99.98	0.99	0.99	3	conclusive
GCF_003003285.1	s__Yoonia maritima	76.7569	73	598	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010667575.1	s__Sulfitobacter sediminilitoris	76.5917	52	598	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001890925.1	s__Planktotalea frisia	76.5775	93	598	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Planktotalea	95.0	99.35	98.99	0.94	0.89	4	-
GCF_000622405.1	s__Sulfitobacter donghicola	76.5179	71	598	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900143545.1	s__Yoonia sp900143545	76.4867	69	598	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000161835.1	s__R2A62 sp000161835	76.4758	104	598	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__R2A62	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115105.1	s__Yoonia tamlensis	76.4269	76	598	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Yoonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000622325.1	s__Sulfitobacter geojensis	76.3958	57	598	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	96.34	96.22	0.90	0.89	35	-
GCF_005771405.1	s__Parasedimentitalea marina_A	76.3228	51	598	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Parasedimentitalea	95.0	97.09	97.09	0.92	0.92	2	-
GCA_017854855.1	s__Sulfitobacter sp017854855	76.1833	50	598	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001458255.1	s__Thalassobius autumnalis	76.1745	66	598	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobius	95.0	99.93	99.93	0.99	0.99	2	-
GCF_001458315.1	s__Thalassobacter stenotrophicus	76.1738	75	598	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Thalassobacter	95.0	98.03	96.21	0.91	0.88	5	-
GCF_900302505.1	s__Pseudoprimorskyibacter insulae	76.11	57	598	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudoprimorskyibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002850435.1	s__Marivivens zhoushanense	76.1024	53	598	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marivivens	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007923355.1	s__Phaeobacter_A marinintestinus	76.0778	52	598	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Phaeobacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000155675.2	s__Octadecabacter antarcticus	75.9731	62	598	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Octadecabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017592335.1	s__Sulfitobacter_F sp017592335	75.8348	52	598	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter_F	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 07:30:47,162] [INFO] GTDB search result was written to OceanDNA-b29548/result_gtdb.tsv
[2023-03-18 07:30:47,162] [INFO] ===== GTDB Search completed =====
[2023-03-18 07:30:47,164] [INFO] DFAST_QC result json was written to OceanDNA-b29548/dqc_result.json
[2023-03-18 07:30:47,164] [INFO] DFAST_QC completed!
[2023-03-18 07:30:47,164] [INFO] Total running time: 0h1m17s