[2023-03-16 03:47:32,868] [INFO] DFAST_QC pipeline started.
[2023-03-16 03:47:32,868] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 03:47:32,868] [INFO] DQC Reference Directory: /var/lib/cwl/stg3c523297-b9d0-42dc-8577-613611eacc10/dqc_reference
[2023-03-16 03:47:34,534] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 03:47:34,535] [INFO] Task started: Prodigal
[2023-03-16 03:47:34,535] [INFO] Running command: cat /var/lib/cwl/stga243efe8-073f-4c40-a818-33a3a8656d09/OceanDNA-b30857.fa | prodigal -d OceanDNA-b30857/cds.fna -a OceanDNA-b30857/protein.faa -g 11 -q > /dev/null
[2023-03-16 03:48:08,042] [INFO] Task succeeded: Prodigal
[2023-03-16 03:48:08,042] [INFO] Task started: HMMsearch
[2023-03-16 03:48:08,042] [INFO] Running command: hmmsearch --tblout OceanDNA-b30857/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3c523297-b9d0-42dc-8577-613611eacc10/dqc_reference/reference_markers.hmm OceanDNA-b30857/protein.faa > /dev/null
[2023-03-16 03:48:08,314] [INFO] Task succeeded: HMMsearch
[2023-03-16 03:48:08,315] [INFO] Found 6/6 markers.
[2023-03-16 03:48:08,346] [INFO] Query marker FASTA was written to OceanDNA-b30857/markers.fasta
[2023-03-16 03:48:08,346] [INFO] Task started: Blastn
[2023-03-16 03:48:08,346] [INFO] Running command: blastn -query OceanDNA-b30857/markers.fasta -db /var/lib/cwl/stg3c523297-b9d0-42dc-8577-613611eacc10/dqc_reference/reference_markers.fasta -out OceanDNA-b30857/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:48:09,012] [INFO] Task succeeded: Blastn
[2023-03-16 03:48:09,013] [INFO] Selected 19 target genomes.
[2023-03-16 03:48:09,013] [INFO] Target genome list was writen to OceanDNA-b30857/target_genomes.txt
[2023-03-16 03:48:09,024] [INFO] Task started: fastANI
[2023-03-16 03:48:09,025] [INFO] Running command: fastANI --query /var/lib/cwl/stga243efe8-073f-4c40-a818-33a3a8656d09/OceanDNA-b30857.fa --refList OceanDNA-b30857/target_genomes.txt --output OceanDNA-b30857/fastani_result.tsv --threads 1
[2023-03-16 03:48:23,246] [INFO] Task succeeded: fastANI
[2023-03-16 03:48:23,246] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3c523297-b9d0-42dc-8577-613611eacc10/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 03:48:23,246] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3c523297-b9d0-42dc-8577-613611eacc10/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 03:48:23,254] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 03:48:23,254] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 03:48:23,254] [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
Thalassospira mesophila	strain=JCM 18969	GCA_002115755.1	1293891	1293891	type	True	86.9547	1291	1717	95	below_threshold
Thalassospira marina	strain=CSC3H3	GCA_002844375.1	2048283	2048283	type	True	82.954	1167	1717	95	below_threshold
Thalassospira xiamenensis	strain=M-5	GCA_000300235.2	220697	220697	suspected-type	True	78.8445	587	1717	95	below_threshold
Thalassospira xiamenensis	strain=DSM 17429	GCA_900156715.1	220697	220697	suspected-type	True	78.7896	593	1717	95	below_threshold
Thalassospira permensis	strain=NBRC 106175	GCA_000714555.1	680197	680197	type	True	78.6957	594	1717	95	below_threshold
Thalassospira alkalitolerans	strain=JCM 18968	GCA_002115745.1	1293890	1293890	type	True	78.3655	623	1717	95	below_threshold
Thalassospira povalilytica	strain=Zumi 95	GCA_002844235.1	732237	732237	type	True	78.2893	581	1717	95	below_threshold
Thalassospira indica	strain=PB8BT	GCA_003403095.1	1891279	1891279	type	True	78.2535	533	1717	95	below_threshold
Thalassospira profundimaris	strain=WP0211	GCA_000300275.1	502049	502049	suspected-type	True	78.1937	527	1717	95	below_threshold
Thalassospira tepidiphila	strain=DSM 18888	GCA_011927685.1	393657	393657	type	True	78.1893	532	1717	95	below_threshold
Thalassospira tepidiphila	strain=MCCC 1A03514	GCA_001662875.1	393657	393657	type	True	78.1519	532	1717	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 03:48:23,254] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30857/tc_result.tsv
[2023-03-16 03:48:23,254] [INFO] ===== Taxonomy check completed =====
[2023-03-16 03:48:23,254] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 03:48:23,254] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3c523297-b9d0-42dc-8577-613611eacc10/dqc_reference/checkm_data
[2023-03-16 03:48:23,255] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 03:48:23,261] [INFO] Task started: CheckM
[2023-03-16 03:48:23,261] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30857/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30857/checkm_input OceanDNA-b30857/checkm_result
[2023-03-16 03:49:43,115] [INFO] Task succeeded: CheckM
[2023-03-16 03:49:43,115] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 03:49:43,119] [INFO] ===== Completeness check finished =====
[2023-03-16 03:49:43,119] [INFO] ===== Start GTDB Search =====
[2023-03-16 03:49:43,119] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30857/markers.fasta)
[2023-03-16 03:49:43,119] [INFO] Task started: Blastn
[2023-03-16 03:49:43,119] [INFO] Running command: blastn -query OceanDNA-b30857/markers.fasta -db /var/lib/cwl/stg3c523297-b9d0-42dc-8577-613611eacc10/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30857/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 03:49:44,559] [INFO] Task succeeded: Blastn
[2023-03-16 03:49:44,560] [INFO] Selected 8 target genomes.
[2023-03-16 03:49:44,560] [INFO] Target genome list was writen to OceanDNA-b30857/target_genomes_gtdb.txt
[2023-03-16 03:49:44,590] [INFO] Task started: fastANI
[2023-03-16 03:49:44,590] [INFO] Running command: fastANI --query /var/lib/cwl/stga243efe8-073f-4c40-a818-33a3a8656d09/OceanDNA-b30857.fa --refList OceanDNA-b30857/target_genomes_gtdb.txt --output OceanDNA-b30857/fastani_result_gtdb.tsv --threads 1
[2023-03-16 03:49:53,241] [INFO] Task succeeded: fastANI
[2023-03-16 03:49:53,247] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 03:49:53,247] [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_002115755.1	s__Thalassospira mesophila	86.9466	1292	1717	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002115825.1	s__Thalassospira sp002115825	86.6904	1342	1717	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001907695.1	s__Thalassospira sp001907695	82.9823	1161	1717	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002844375.1	s__Thalassospira marina	82.9613	1166	1717	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	97.72	97.72	0.93	0.93	2	-
GCF_003326755.1	s__Thalassospira profundimaris_B	82.5414	1131	1717	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002115745.1	s__Thalassospira alkalitolerans	78.3741	621	1717	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003403095.1	s__Thalassospira indica	78.2775	529	1717	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002844235.1	s__Thalassospira povalilytica	78.2749	582	1717	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Thalassospiraceae;g__Thalassospira	95.0	97.81	97.62	0.94	0.91	8	-
--------------------------------------------------------------------------------
[2023-03-16 03:49:53,247] [INFO] GTDB search result was written to OceanDNA-b30857/result_gtdb.tsv
[2023-03-16 03:49:53,247] [INFO] ===== GTDB Search completed =====
[2023-03-16 03:49:53,249] [INFO] DFAST_QC result json was written to OceanDNA-b30857/dqc_result.json
[2023-03-16 03:49:53,249] [INFO] DFAST_QC completed!
[2023-03-16 03:49:53,249] [INFO] Total running time: 0h2m20s