[2023-03-16 15:26:08,197] [INFO] DFAST_QC pipeline started.
[2023-03-16 15:26:08,197] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 15:26:08,197] [INFO] DQC Reference Directory: /var/lib/cwl/stge6ebaaf3-cecf-4ae9-b513-23c1ebaa7469/dqc_reference
[2023-03-16 15:26:09,503] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 15:26:09,503] [INFO] Task started: Prodigal
[2023-03-16 15:26:09,503] [INFO] Running command: cat /var/lib/cwl/stg495052a3-877d-4f23-86d0-3a0bf6dde2cf/OceanDNA-b2819.fa | prodigal -d OceanDNA-b2819/cds.fna -a OceanDNA-b2819/protein.faa -g 11 -q > /dev/null
[2023-03-16 15:26:28,165] [INFO] Task succeeded: Prodigal
[2023-03-16 15:26:28,165] [INFO] Task started: HMMsearch
[2023-03-16 15:26:28,165] [INFO] Running command: hmmsearch --tblout OceanDNA-b2819/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge6ebaaf3-cecf-4ae9-b513-23c1ebaa7469/dqc_reference/reference_markers.hmm OceanDNA-b2819/protein.faa > /dev/null
[2023-03-16 15:26:28,552] [INFO] Task succeeded: HMMsearch
[2023-03-16 15:26:28,553] [INFO] Found 6/6 markers.
[2023-03-16 15:26:28,578] [INFO] Query marker FASTA was written to OceanDNA-b2819/markers.fasta
[2023-03-16 15:26:28,578] [INFO] Task started: Blastn
[2023-03-16 15:26:28,579] [INFO] Running command: blastn -query OceanDNA-b2819/markers.fasta -db /var/lib/cwl/stge6ebaaf3-cecf-4ae9-b513-23c1ebaa7469/dqc_reference/reference_markers.fasta -out OceanDNA-b2819/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 15:26:32,038] [INFO] Task succeeded: Blastn
[2023-03-16 15:26:32,039] [INFO] Selected 16 target genomes.
[2023-03-16 15:26:32,039] [INFO] Target genome list was writen to OceanDNA-b2819/target_genomes.txt
[2023-03-16 15:26:32,046] [INFO] Task started: fastANI
[2023-03-16 15:26:32,046] [INFO] Running command: fastANI --query /var/lib/cwl/stg495052a3-877d-4f23-86d0-3a0bf6dde2cf/OceanDNA-b2819.fa --refList OceanDNA-b2819/target_genomes.txt --output OceanDNA-b2819/fastani_result.tsv --threads 1
[2023-03-16 15:26:47,744] [INFO] Task succeeded: fastANI
[2023-03-16 15:26:47,744] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge6ebaaf3-cecf-4ae9-b513-23c1ebaa7469/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 15:26:47,744] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge6ebaaf3-cecf-4ae9-b513-23c1ebaa7469/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 15:26:47,754] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 15:26:47,754] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 15:26:47,754] [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
Chryseoglobus frigidaquae	strain=DSM 23889	GCA_014200395.1	424758	424758	type	True	89.9971	651	795	95	below_threshold
Chryseoglobus frigidaquae	strain=DSM 23889	GCA_009664385.2	424758	424758	type	True	89.9919	646	795	95	below_threshold
Microcella putealis	strain=CV2	GCA_004216575.1	337005	337005	type	True	81.4681	478	795	95	below_threshold
Microcella putealis	strain=DSM 19627	GCA_006716545.1	337005	337005	type	True	81.3214	482	795	95	below_threshold
Microcella alkaliphila	strain=AC4r	GCA_004216855.1	279828	279828	type	True	81.1506	480	795	95	below_threshold
Protaetiibacter intestinalis	strain=2DFWR-13	GCA_003627075.1	2419774	2419774	type	True	80.2185	418	795	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	79.5953	416	795	95	below_threshold
Agromyces flavus	strain=CPCC 202695	GCA_004366335.2	589382	589382	type	True	79.45	382	795	95	below_threshold
Agromyces agglutinans	strain=CFH 90414	GCA_009647605.1	2662258	2662258	type	True	79.4103	392	795	95	below_threshold
Agromyces mediolanus	strain=JCM 3346	GCA_014648575.1	41986	41986	type	True	79.2425	428	795	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_021922985.1	31965	28447	type	True	79.1984	350	795	95	below_threshold
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	79.1385	396	795	95	below_threshold
Agromyces marinus	strain=DSM 26151	GCA_021442325.1	1389020	1389020	type	True	79.1338	378	795	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_002240635.1	31965	28447	type	True	79.1288	358	795	95	below_threshold
Agromyces ramosus	strain=DSM 43045	GCA_004216665.1	33879	33879	type	True	79.0913	397	795	95	below_threshold
Clavibacter zhangzhiyongii	strain=DM1	GCA_014775655.1	2768071	2768071	type	True	79.0779	354	795	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 15:26:47,754] [INFO] DFAST Taxonomy check result was written to OceanDNA-b2819/tc_result.tsv
[2023-03-16 15:26:47,754] [INFO] ===== Taxonomy check completed =====
[2023-03-16 15:26:47,754] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 15:26:47,754] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge6ebaaf3-cecf-4ae9-b513-23c1ebaa7469/dqc_reference/checkm_data
[2023-03-16 15:26:47,755] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 15:26:47,759] [INFO] Task started: CheckM
[2023-03-16 15:26:47,759] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b2819/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b2819/checkm_input OceanDNA-b2819/checkm_result
[2023-03-16 15:27:30,550] [INFO] Task succeeded: CheckM
[2023-03-16 15:27:30,551] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 15:27:30,553] [INFO] ===== Completeness check finished =====
[2023-03-16 15:27:30,553] [INFO] ===== Start GTDB Search =====
[2023-03-16 15:27:30,553] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b2819/markers.fasta)
[2023-03-16 15:27:30,553] [INFO] Task started: Blastn
[2023-03-16 15:27:30,553] [INFO] Running command: blastn -query OceanDNA-b2819/markers.fasta -db /var/lib/cwl/stge6ebaaf3-cecf-4ae9-b513-23c1ebaa7469/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b2819/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 15:27:33,161] [INFO] Task succeeded: Blastn
[2023-03-16 15:27:33,162] [INFO] Selected 12 target genomes.
[2023-03-16 15:27:33,162] [INFO] Target genome list was writen to OceanDNA-b2819/target_genomes_gtdb.txt
[2023-03-16 15:27:33,532] [INFO] Task started: fastANI
[2023-03-16 15:27:33,532] [INFO] Running command: fastANI --query /var/lib/cwl/stg495052a3-877d-4f23-86d0-3a0bf6dde2cf/OceanDNA-b2819.fa --refList OceanDNA-b2819/target_genomes_gtdb.txt --output OceanDNA-b2819/fastani_result_gtdb.tsv --threads 1
[2023-03-16 15:27:46,625] [INFO] Task succeeded: fastANI
[2023-03-16 15:27:46,632] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 15:27:46,632] [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_014200395.1	s__Chryseoglobus frigidaquae	89.9971	651	795	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Chryseoglobus	95.0	100.00	100.00	1.00	1.00	2	-
GCA_001464255.1	s__Chryseoglobus sp001464255	86.6553	435	795	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Chryseoglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002280615.1	s__Chryseoglobus sp002280615	86.5074	352	795	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Chryseoglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014595885.1	s__Yonghaparkia alkaliphila_A	83.9478	563	795	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Yonghaparkia	95.0	100.00	100.00	1.00	1.00	2	-
GCA_005778835.1	s__Chryseoglobus sp005778835	83.6971	526	795	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Chryseoglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425665.1	s__Yonghaparkia sp001425665	83.2104	547	795	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Yonghaparkia	95.0	99.25	99.25	0.97	0.97	2	-
GCA_012530535.1	s__Yonghaparkia sp012530535	82.9438	543	795	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Yonghaparkia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013297625.1	s__Chryseoglobus sp013297625	82.9204	487	795	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Chryseoglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013823625.1	s__Chryseoglobus sp013823625	82.9105	565	795	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Chryseoglobus	95.0	100.00	100.00	1.00	1.00	2	-
GCA_005502445.1	s__Yonghaparkia sp005502445	82.8337	479	795	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Yonghaparkia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013414345.1	s__Marinisubtilis indicus	82.4103	525	795	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Marinisubtilis	95.0	96.33	95.90	0.85	0.83	6	-
GCA_005777405.1	s__Chryseoglobus sp005777405	81.3158	425	795	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Chryseoglobus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 15:27:46,633] [INFO] GTDB search result was written to OceanDNA-b2819/result_gtdb.tsv
[2023-03-16 15:27:46,633] [INFO] ===== GTDB Search completed =====
[2023-03-16 15:27:46,634] [INFO] DFAST_QC result json was written to OceanDNA-b2819/dqc_result.json
[2023-03-16 15:27:46,634] [INFO] DFAST_QC completed!
[2023-03-16 15:27:46,634] [INFO] Total running time: 0h1m38s