[2023-03-17 05:53:20,812] [INFO] DFAST_QC pipeline started.
[2023-03-17 05:53:20,812] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 05:53:20,812] [INFO] DQC Reference Directory: /var/lib/cwl/stg2664bce4-bbc5-4c31-b1d9-28d1eca0f081/dqc_reference
[2023-03-17 05:53:21,924] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 05:53:21,925] [INFO] Task started: Prodigal
[2023-03-17 05:53:21,925] [INFO] Running command: cat /var/lib/cwl/stg67645db8-099f-4f36-8ecd-a6d7f8bf592f/OceanDNA-b1294.fa | prodigal -d OceanDNA-b1294/cds.fna -a OceanDNA-b1294/protein.faa -g 11 -q > /dev/null
[2023-03-17 05:53:39,668] [INFO] Task succeeded: Prodigal
[2023-03-17 05:53:39,668] [INFO] Task started: HMMsearch
[2023-03-17 05:53:39,668] [INFO] Running command: hmmsearch --tblout OceanDNA-b1294/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2664bce4-bbc5-4c31-b1d9-28d1eca0f081/dqc_reference/reference_markers.hmm OceanDNA-b1294/protein.faa > /dev/null
[2023-03-17 05:53:39,832] [INFO] Task succeeded: HMMsearch
[2023-03-17 05:53:39,833] [INFO] Found 6/6 markers.
[2023-03-17 05:53:39,848] [INFO] Query marker FASTA was written to OceanDNA-b1294/markers.fasta
[2023-03-17 05:53:39,849] [INFO] Task started: Blastn
[2023-03-17 05:53:39,849] [INFO] Running command: blastn -query OceanDNA-b1294/markers.fasta -db /var/lib/cwl/stg2664bce4-bbc5-4c31-b1d9-28d1eca0f081/dqc_reference/reference_markers.fasta -out OceanDNA-b1294/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:53:40,520] [INFO] Task succeeded: Blastn
[2023-03-17 05:53:40,521] [INFO] Selected 26 target genomes.
[2023-03-17 05:53:40,522] [INFO] Target genome list was writen to OceanDNA-b1294/target_genomes.txt
[2023-03-17 05:53:40,591] [INFO] Task started: fastANI
[2023-03-17 05:53:40,591] [INFO] Running command: fastANI --query /var/lib/cwl/stg67645db8-099f-4f36-8ecd-a6d7f8bf592f/OceanDNA-b1294.fa --refList OceanDNA-b1294/target_genomes.txt --output OceanDNA-b1294/fastani_result.tsv --threads 1
[2023-03-17 05:53:58,708] [INFO] Task succeeded: fastANI
[2023-03-17 05:53:58,709] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2664bce4-bbc5-4c31-b1d9-28d1eca0f081/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 05:53:58,709] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2664bce4-bbc5-4c31-b1d9-28d1eca0f081/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 05:53:58,716] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 05:53:58,716] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 05:53:58,716] [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
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	76.9892	136	605	95	below_threshold
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	76.727	146	605	95	below_threshold
Rhabdothermincola sediminis	strain=SYSU G02662	GCA_014805525.1	2751370	2751370	type	True	76.3983	106	605	95	below_threshold
Ilumatobacter nonamiensis	strain=YM16-303	GCA_000350145.1	467093	467093	type	True	76.0538	56	605	95	below_threshold
Ilumatobacter coccineus	strain=YM16-304	GCA_000348785.1	467094	467094	type	True	76.0057	60	605	95	below_threshold
Nocardioides ungokensis	strain=LMG 28591	GCA_013466985.1	1643322	1643322	type	True	75.3157	50	605	95	below_threshold
Streptacidiphilus carbonis	strain=NBRC 100919	GCA_000787775.1	105422	105422	type	True	75.2359	70	605	95	below_threshold
Micromonospora zamorensis	strain=DSM 45600	GCA_900090275.1	709883	709883	type	True	75.2054	59	605	95	below_threshold
Kitasatospora purpeofusca	strain=NRRL B-1817	GCA_000718025.1	67352	67352	type	True	75.0966	90	605	95	below_threshold
Azospirillum halopraeferens	strain=DSM 3675	GCA_000429625.1	34010	34010	type	True	74.6449	52	605	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 05:53:58,722] [INFO] DFAST Taxonomy check result was written to OceanDNA-b1294/tc_result.tsv
[2023-03-17 05:53:58,729] [INFO] ===== Taxonomy check completed =====
[2023-03-17 05:53:58,729] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 05:53:58,729] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2664bce4-bbc5-4c31-b1d9-28d1eca0f081/dqc_reference/checkm_data
[2023-03-17 05:53:58,730] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 05:53:58,734] [INFO] Task started: CheckM
[2023-03-17 05:53:58,734] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b1294/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b1294/checkm_input OceanDNA-b1294/checkm_result
[2023-03-17 05:54:37,329] [INFO] Task succeeded: CheckM
[2023-03-17 05:54:37,329] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 96.30%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 05:54:37,368] [INFO] ===== Completeness check finished =====
[2023-03-17 05:54:37,368] [INFO] ===== Start GTDB Search =====
[2023-03-17 05:54:37,369] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b1294/markers.fasta)
[2023-03-17 05:54:37,370] [INFO] Task started: Blastn
[2023-03-17 05:54:37,370] [INFO] Running command: blastn -query OceanDNA-b1294/markers.fasta -db /var/lib/cwl/stg2664bce4-bbc5-4c31-b1d9-28d1eca0f081/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b1294/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:54:38,509] [INFO] Task succeeded: Blastn
[2023-03-17 05:54:38,512] [INFO] Selected 12 target genomes.
[2023-03-17 05:54:38,512] [INFO] Target genome list was writen to OceanDNA-b1294/target_genomes_gtdb.txt
[2023-03-17 05:54:38,519] [INFO] Task started: fastANI
[2023-03-17 05:54:38,519] [INFO] Running command: fastANI --query /var/lib/cwl/stg67645db8-099f-4f36-8ecd-a6d7f8bf592f/OceanDNA-b1294.fa --refList OceanDNA-b1294/target_genomes_gtdb.txt --output OceanDNA-b1294/fastani_result_gtdb.tsv --threads 1
[2023-03-17 05:54:43,603] [INFO] Task succeeded: fastANI
[2023-03-17 05:54:43,610] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 05:54:43,610] [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_012961035.1	s__UBA9410 sp012961035	92.6873	513	605	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	99.67	99.67	0.93	0.93	2	-
GCA_014240365.1	s__UBA9410 sp014240365	89.3226	498	605	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	98.11	98.07	0.86	0.84	5	-
GCA_016845305.1	s__UBA9410 sp016845305	80.5564	428	605	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014239855.1	s__UBA9410 sp014239855	80.2503	417	605	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002727895.1	s__UBA9410 sp002727895	79.7614	299	605	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	97.12	97.12	0.93	0.93	2	-
GCA_014237715.1	s__UBA9410 sp014237715	79.4705	349	605	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	98.52	98.52	0.97	0.97	2	-
GCA_002346745.1	s__S20-B6 sp002346745	79.1226	315	605	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__S20-B6	95.0	97.72	96.97	0.85	0.81	8	-
GCA_002699725.1	s__S20-B6 sp002699725	78.9872	268	605	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__S20-B6	95.0	98.58	98.41	0.87	0.86	3	-
GCA_014381945.1	s__S20-B6 sp014381945	78.4668	276	605	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__S20-B6	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002714485.1	s__UBA9410 sp002714485	78.2724	233	605	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002365325.1	s__UBA3125 sp002365325	77.5776	160	605	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA3125	95.0	98.82	97.98	0.79	0.76	7	-
--------------------------------------------------------------------------------
[2023-03-17 05:54:43,610] [INFO] GTDB search result was written to OceanDNA-b1294/result_gtdb.tsv
[2023-03-17 05:54:43,610] [INFO] ===== GTDB Search completed =====
[2023-03-17 05:54:43,612] [INFO] DFAST_QC result json was written to OceanDNA-b1294/dqc_result.json
[2023-03-17 05:54:43,612] [INFO] DFAST_QC completed!
[2023-03-17 05:54:43,612] [INFO] Total running time: 0h1m23s