[2023-03-17 23:49:09,985] [INFO] DFAST_QC pipeline started.
[2023-03-17 23:49:09,988] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 23:49:09,988] [INFO] DQC Reference Directory: /var/lib/cwl/stg89b5d97f-2fc8-4be0-b018-fcbae67fe5e0/dqc_reference
[2023-03-17 23:49:11,099] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 23:49:11,100] [INFO] Task started: Prodigal
[2023-03-17 23:49:11,100] [INFO] Running command: cat /var/lib/cwl/stg7b6615a6-9ab4-430c-a687-8f9cba8d7f66/OceanDNA-b1338.fa | prodigal -d OceanDNA-b1338/cds.fna -a OceanDNA-b1338/protein.faa -g 11 -q > /dev/null
[2023-03-17 23:49:19,540] [INFO] Task succeeded: Prodigal
[2023-03-17 23:49:19,540] [INFO] Task started: HMMsearch
[2023-03-17 23:49:19,540] [INFO] Running command: hmmsearch --tblout OceanDNA-b1338/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg89b5d97f-2fc8-4be0-b018-fcbae67fe5e0/dqc_reference/reference_markers.hmm OceanDNA-b1338/protein.faa > /dev/null
[2023-03-17 23:49:19,688] [INFO] Task succeeded: HMMsearch
[2023-03-17 23:49:19,688] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg7b6615a6-9ab4-430c-a687-8f9cba8d7f66/OceanDNA-b1338.fa]
[2023-03-17 23:49:19,725] [INFO] Query marker FASTA was written to OceanDNA-b1338/markers.fasta
[2023-03-17 23:49:19,726] [INFO] Task started: Blastn
[2023-03-17 23:49:19,726] [INFO] Running command: blastn -query OceanDNA-b1338/markers.fasta -db /var/lib/cwl/stg89b5d97f-2fc8-4be0-b018-fcbae67fe5e0/dqc_reference/reference_markers.fasta -out OceanDNA-b1338/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:49:20,294] [INFO] Task succeeded: Blastn
[2023-03-17 23:49:20,301] [INFO] Selected 15 target genomes.
[2023-03-17 23:49:20,302] [INFO] Target genome list was writen to OceanDNA-b1338/target_genomes.txt
[2023-03-17 23:49:20,311] [INFO] Task started: fastANI
[2023-03-17 23:49:20,311] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b6615a6-9ab4-430c-a687-8f9cba8d7f66/OceanDNA-b1338.fa --refList OceanDNA-b1338/target_genomes.txt --output OceanDNA-b1338/fastani_result.tsv --threads 1
[2023-03-17 23:49:32,213] [INFO] Task succeeded: fastANI
[2023-03-17 23:49:32,214] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg89b5d97f-2fc8-4be0-b018-fcbae67fe5e0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 23:49:32,214] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg89b5d97f-2fc8-4be0-b018-fcbae67fe5e0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 23:49:32,220] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 23:49:32,221] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 23:49:32,221] [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
Rhabdothermincola salaria	strain=EGI L10124	GCA_021246445.1	2903142	2903142	type	True	77.1314	108	378	95	below_threshold
Actinomarinicola tropica	strain=SCSIO 58843	GCA_009650215.1	2789776	2789776	type	True	76.9143	99	378	95	below_threshold
Rhabdothermincola sediminis	strain=SYSU G02662	GCA_014805525.1	2751370	2751370	type	True	76.6376	76	378	95	below_threshold
Desertimonas flava	strain=SYSU D60003	GCA_003426815.1	2064846	2064846	type	True	76.0237	82	378	95	below_threshold
Ilumatobacter coccineus	strain=YM16-304	GCA_000348785.1	467094	467094	type	True	75.6733	51	378	95	below_threshold
Ilumatobacter fluminis	strain=DSM 18936	GCA_004364865.1	467091	467091	type	True	75.6256	68	378	95	below_threshold
Asanoa iriomotensis	strain=NBRC 100142	GCA_016862515.1	234613	234613	type	True	74.9295	70	378	95	below_threshold
Actinomadura violacea	strain=LCR2-06	GCA_017573465.1	2819934	2819934	type	True	74.7193	59	378	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 23:49:32,221] [INFO] DFAST Taxonomy check result was written to OceanDNA-b1338/tc_result.tsv
[2023-03-17 23:49:32,221] [INFO] ===== Taxonomy check completed =====
[2023-03-17 23:49:32,221] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 23:49:32,221] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg89b5d97f-2fc8-4be0-b018-fcbae67fe5e0/dqc_reference/checkm_data
[2023-03-17 23:49:32,222] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 23:49:32,225] [INFO] Task started: CheckM
[2023-03-17 23:49:32,225] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b1338/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b1338/checkm_input OceanDNA-b1338/checkm_result
[2023-03-17 23:49:58,182] [INFO] Task succeeded: CheckM
[2023-03-17 23:49:58,183] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.12%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 23:49:58,202] [INFO] ===== Completeness check finished =====
[2023-03-17 23:49:58,202] [INFO] ===== Start GTDB Search =====
[2023-03-17 23:49:58,202] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b1338/markers.fasta)
[2023-03-17 23:49:58,202] [INFO] Task started: Blastn
[2023-03-17 23:49:58,202] [INFO] Running command: blastn -query OceanDNA-b1338/markers.fasta -db /var/lib/cwl/stg89b5d97f-2fc8-4be0-b018-fcbae67fe5e0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b1338/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:49:58,873] [INFO] Task succeeded: Blastn
[2023-03-17 23:49:58,880] [INFO] Selected 12 target genomes.
[2023-03-17 23:49:58,880] [INFO] Target genome list was writen to OceanDNA-b1338/target_genomes_gtdb.txt
[2023-03-17 23:49:58,887] [INFO] Task started: fastANI
[2023-03-17 23:49:58,887] [INFO] Running command: fastANI --query /var/lib/cwl/stg7b6615a6-9ab4-430c-a687-8f9cba8d7f66/OceanDNA-b1338.fa --refList OceanDNA-b1338/target_genomes_gtdb.txt --output OceanDNA-b1338/fastani_result_gtdb.tsv --threads 1
[2023-03-17 23:50:03,835] [INFO] Task succeeded: fastANI
[2023-03-17 23:50:03,841] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 23:50:03,842] [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_002727895.1	s__UBA9410 sp002727895	99.2783	324	378	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	97.12	97.12	0.93	0.93	2	conclusive
GCA_016845305.1	s__UBA9410 sp016845305	88.5513	333	378	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	82.162	274	378	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_014237715.1	s__UBA9410 sp014237715	80.7683	256	378	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	80.3618	204	378	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_012961035.1	s__UBA9410 sp012961035	80.0313	224	378	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_003541675.1	s__UBA9410 sp003541675	79.9601	169	378	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_002717365.1	s__UBA9410 sp002717365	79.719	149	378	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_002348705.1	s__UBA9410 sp002348705	78.6605	182	378	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__MedAcidi-G1;g__UBA9410	95.0	99.53	98.86	0.93	0.89	6	-
GCA_016649895.1	s__Actinomarinicola sp016649895	77.472	80	378	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__SKKL01;g__Actinomarinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003697065.1	s__J010 sp003697065	76.7007	107	378	d__Bacteria;p__Actinobacteriota;c__Acidimicrobiia;o__Acidimicrobiales;f__UBA11606;g__J010	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 23:50:03,846] [INFO] GTDB search result was written to OceanDNA-b1338/result_gtdb.tsv
[2023-03-17 23:50:03,848] [INFO] ===== GTDB Search completed =====
[2023-03-17 23:50:03,849] [INFO] DFAST_QC result json was written to OceanDNA-b1338/dqc_result.json
[2023-03-17 23:50:03,850] [INFO] DFAST_QC completed!
[2023-03-17 23:50:03,850] [INFO] Total running time: 0h0m54s