[2023-03-18 04:37:59,262] [INFO] DFAST_QC pipeline started.
[2023-03-18 04:37:59,263] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 04:37:59,263] [INFO] DQC Reference Directory: /var/lib/cwl/stgb344480b-6080-49c5-8836-5acddddfbad1/dqc_reference
[2023-03-18 04:38:00,371] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 04:38:00,371] [INFO] Task started: Prodigal
[2023-03-18 04:38:00,371] [INFO] Running command: cat /var/lib/cwl/stgbdd49911-513d-44c8-ae55-45dadb8e59fb/OceanDNA-b30006.fa | prodigal -d OceanDNA-b30006/cds.fna -a OceanDNA-b30006/protein.faa -g 11 -q > /dev/null
[2023-03-18 04:38:28,530] [INFO] Task succeeded: Prodigal
[2023-03-18 04:38:28,531] [INFO] Task started: HMMsearch
[2023-03-18 04:38:28,531] [INFO] Running command: hmmsearch --tblout OceanDNA-b30006/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb344480b-6080-49c5-8836-5acddddfbad1/dqc_reference/reference_markers.hmm OceanDNA-b30006/protein.faa > /dev/null
[2023-03-18 04:38:28,733] [INFO] Task succeeded: HMMsearch
[2023-03-18 04:38:28,733] [INFO] Found 6/6 markers.
[2023-03-18 04:38:28,759] [INFO] Query marker FASTA was written to OceanDNA-b30006/markers.fasta
[2023-03-18 04:38:28,760] [INFO] Task started: Blastn
[2023-03-18 04:38:28,761] [INFO] Running command: blastn -query OceanDNA-b30006/markers.fasta -db /var/lib/cwl/stgb344480b-6080-49c5-8836-5acddddfbad1/dqc_reference/reference_markers.fasta -out OceanDNA-b30006/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:38:29,556] [INFO] Task succeeded: Blastn
[2023-03-18 04:38:29,557] [INFO] Selected 8 target genomes.
[2023-03-18 04:38:29,557] [INFO] Target genome list was writen to OceanDNA-b30006/target_genomes.txt
[2023-03-18 04:38:29,563] [INFO] Task started: fastANI
[2023-03-18 04:38:29,563] [INFO] Running command: fastANI --query /var/lib/cwl/stgbdd49911-513d-44c8-ae55-45dadb8e59fb/OceanDNA-b30006.fa --refList OceanDNA-b30006/target_genomes.txt --output OceanDNA-b30006/fastani_result.tsv --threads 1
[2023-03-18 04:38:36,996] [INFO] Task succeeded: fastANI
[2023-03-18 04:38:36,996] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb344480b-6080-49c5-8836-5acddddfbad1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 04:38:36,996] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb344480b-6080-49c5-8836-5acddddfbad1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 04:38:37,003] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 04:38:37,003] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 04:38:37,003] [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
Pseudooceanicola marinus	strain=LMG 23705	GCA_002786295.1	396013	396013	type	True	83.8467	953	1534	95	below_threshold
Pseudooceanicola marinus	strain=CECT 7751	GCA_900172385.1	396013	396013	type	True	83.7678	969	1534	95	below_threshold
Pseudooceanicola antarcticus	strain=CGMCC 1.12662	GCA_900215355.1	1247613	1247613	type	True	83.1166	880	1534	95	below_threshold
Pseudooceanicola antarcticus	strain=Ar-45	GCA_002786285.1	1247613	1247613	type	True	83.0558	883	1534	95	below_threshold
Pseudooceanicola endophyticus	strain=CBS1P-1	GCA_018760365.1	2841273	2841273	type	True	81.6222	861	1534	95	below_threshold
Pseudooceanicola algae	strain=Lw-13e	GCA_003590145.2	1537215	1537215	type	True	79.8147	631	1534	95	below_threshold
Pseudooceanicola onchidii	strain=XY-99	GCA_004959925.1	2562279	2562279	type	True	79.3369	584	1534	95	below_threshold
Yangia pacifica	strain=DSM 26894	GCA_900116195.1	311180	311180	suspected-type	True	79.2157	623	1534	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 04:38:37,003] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30006/tc_result.tsv
[2023-03-18 04:38:37,003] [INFO] ===== Taxonomy check completed =====
[2023-03-18 04:38:37,003] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 04:38:37,003] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb344480b-6080-49c5-8836-5acddddfbad1/dqc_reference/checkm_data
[2023-03-18 04:38:37,004] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 04:38:37,334] [INFO] Task started: CheckM
[2023-03-18 04:38:37,334] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30006/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30006/checkm_input OceanDNA-b30006/checkm_result
[2023-03-18 04:40:10,481] [INFO] Task succeeded: CheckM
[2023-03-18 04:40:10,482] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 04:40:10,484] [INFO] ===== Completeness check finished =====
[2023-03-18 04:40:10,484] [INFO] ===== Start GTDB Search =====
[2023-03-18 04:40:10,484] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30006/markers.fasta)
[2023-03-18 04:40:10,485] [INFO] Task started: Blastn
[2023-03-18 04:40:10,485] [INFO] Running command: blastn -query OceanDNA-b30006/markers.fasta -db /var/lib/cwl/stgb344480b-6080-49c5-8836-5acddddfbad1/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30006/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 04:40:11,870] [INFO] Task succeeded: Blastn
[2023-03-18 04:40:11,871] [INFO] Selected 8 target genomes.
[2023-03-18 04:40:11,871] [INFO] Target genome list was writen to OceanDNA-b30006/target_genomes_gtdb.txt
[2023-03-18 04:40:11,900] [INFO] Task started: fastANI
[2023-03-18 04:40:11,900] [INFO] Running command: fastANI --query /var/lib/cwl/stgbdd49911-513d-44c8-ae55-45dadb8e59fb/OceanDNA-b30006.fa --refList OceanDNA-b30006/target_genomes_gtdb.txt --output OceanDNA-b30006/fastani_result_gtdb.tsv --threads 1
[2023-03-18 04:40:19,902] [INFO] Task succeeded: fastANI
[2023-03-18 04:40:19,908] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 04:40:19,908] [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_002786295.1	s__Pseudooceanicola marinus	83.8368	954	1534	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.99	99.99	0.99	0.99	2	-
GCA_018222585.1	s__Pseudooceanicola sp018222585	83.296	916	1534	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.94	99.94	0.96	0.96	2	-
GCF_000220565.1	s__Pseudooceanicola sp000220565	83.2473	854	1534	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900215355.1	s__Pseudooceanicola antarcticus	83.1027	882	1534	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009827095.1	s__Pseudooceanicola sp009827095	81.5867	858	1534	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	99.99	99.99	0.98	0.98	2	-
GCF_011806405.1	s__Pseudooceanicola sp011806405	80.5681	707	1534	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003590145.2	s__Pseudooceanicola algae	79.8064	632	1534	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004959925.1	s__Pseudooceanicola onchidii	79.3538	582	1534	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Pseudooceanicola	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 04:40:19,908] [INFO] GTDB search result was written to OceanDNA-b30006/result_gtdb.tsv
[2023-03-18 04:40:19,908] [INFO] ===== GTDB Search completed =====
[2023-03-18 04:40:19,909] [INFO] DFAST_QC result json was written to OceanDNA-b30006/dqc_result.json
[2023-03-18 04:40:19,909] [INFO] DFAST_QC completed!
[2023-03-18 04:40:19,909] [INFO] Total running time: 0h2m21s