[2023-03-17 03:50:15,877] [INFO] DFAST_QC pipeline started.
[2023-03-17 03:50:15,877] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 03:50:15,877] [INFO] DQC Reference Directory: /var/lib/cwl/stg2d8579c0-ea29-438b-8750-4da72ffc8da0/dqc_reference
[2023-03-17 03:50:17,015] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 03:50:17,015] [INFO] Task started: Prodigal
[2023-03-17 03:50:17,015] [INFO] Running command: cat /var/lib/cwl/stg77d54b8c-9ad2-49de-852a-52a4ed72f6c0/OceanDNA-b41572.fa | prodigal -d OceanDNA-b41572/cds.fna -a OceanDNA-b41572/protein.faa -g 11 -q > /dev/null
[2023-03-17 03:50:38,944] [INFO] Task succeeded: Prodigal
[2023-03-17 03:50:38,944] [INFO] Task started: HMMsearch
[2023-03-17 03:50:38,944] [INFO] Running command: hmmsearch --tblout OceanDNA-b41572/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2d8579c0-ea29-438b-8750-4da72ffc8da0/dqc_reference/reference_markers.hmm OceanDNA-b41572/protein.faa > /dev/null
[2023-03-17 03:50:39,203] [INFO] Task succeeded: HMMsearch
[2023-03-17 03:50:39,204] [INFO] Found 6/6 markers.
[2023-03-17 03:50:39,228] [INFO] Query marker FASTA was written to OceanDNA-b41572/markers.fasta
[2023-03-17 03:50:39,228] [INFO] Task started: Blastn
[2023-03-17 03:50:39,228] [INFO] Running command: blastn -query OceanDNA-b41572/markers.fasta -db /var/lib/cwl/stg2d8579c0-ea29-438b-8750-4da72ffc8da0/dqc_reference/reference_markers.fasta -out OceanDNA-b41572/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:50:39,898] [INFO] Task succeeded: Blastn
[2023-03-17 03:50:39,899] [INFO] Selected 24 target genomes.
[2023-03-17 03:50:39,900] [INFO] Target genome list was writen to OceanDNA-b41572/target_genomes.txt
[2023-03-17 03:50:39,914] [INFO] Task started: fastANI
[2023-03-17 03:50:39,915] [INFO] Running command: fastANI --query /var/lib/cwl/stg77d54b8c-9ad2-49de-852a-52a4ed72f6c0/OceanDNA-b41572.fa --refList OceanDNA-b41572/target_genomes.txt --output OceanDNA-b41572/fastani_result.tsv --threads 1
[2023-03-17 03:50:54,195] [INFO] Task succeeded: fastANI
[2023-03-17 03:50:54,195] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2d8579c0-ea29-438b-8750-4da72ffc8da0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 03:50:54,195] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2d8579c0-ea29-438b-8750-4da72ffc8da0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 03:50:54,203] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 03:50:54,203] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-17 03:50:54,203] [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
Zhongshania aliphaticivorans	strain=SM-2	GCA_001586255.1	1470434	1470434	type	True	79.4714	379	1253	95	below_threshold
Zhongshania antarctica	strain=ZS5-23	GCA_014898265.1	641702	641702	type	True	79.0874	367	1253	95	below_threshold
Zhongshania antarctica	strain=DSM 25701	GCA_014202945.1	641702	641702	type	True	79.0548	375	1253	95	below_threshold
Spongiibacter thalassae	strain=KMU-166	GCA_012272835.1	2721624	2721624	type	True	77.7868	162	1253	95	below_threshold
Spongiibacter nanhainus	strain=csc3.9	GCA_016132545.1	2794344	2794344	type	True	77.5343	127	1253	95	below_threshold
Spongiibacter taiwanensis	strain=SPT1	GCA_023702635.1	1748242	1748242	type	True	77.2882	137	1253	95	below_threshold
Spongiibacter pelagi	strain=KMU-158	GCA_014705705.1	2760804	2760804	type	True	77.0984	171	1253	95	below_threshold
Spongiibacter tropicus	strain=DSM 19543	GCA_000420325.1	454602	454602	type	True	77.0869	142	1253	95	below_threshold
Litorivivens lipolytica	strain=CECT 8654	GCA_014191715.1	1524264	1524264	type	True	76.5785	82	1253	95	below_threshold
Oceanicoccus sagamiensis	strain=NBRC 107125	GCA_002117105.1	716816	716816	type	True	75.8455	50	1253	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-17 03:50:54,203] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41572/tc_result.tsv
[2023-03-17 03:50:54,203] [INFO] ===== Taxonomy check completed =====
[2023-03-17 03:50:54,203] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 03:50:54,203] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2d8579c0-ea29-438b-8750-4da72ffc8da0/dqc_reference/checkm_data
[2023-03-17 03:50:54,204] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 03:50:54,209] [INFO] Task started: CheckM
[2023-03-17 03:50:54,209] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41572/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41572/checkm_input OceanDNA-b41572/checkm_result
[2023-03-17 03:51:48,992] [INFO] Task succeeded: CheckM
[2023-03-17 03:51:48,993] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 03:51:48,996] [INFO] ===== Completeness check finished =====
[2023-03-17 03:51:48,996] [INFO] ===== Start GTDB Search =====
[2023-03-17 03:51:48,996] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41572/markers.fasta)
[2023-03-17 03:51:48,996] [INFO] Task started: Blastn
[2023-03-17 03:51:48,996] [INFO] Running command: blastn -query OceanDNA-b41572/markers.fasta -db /var/lib/cwl/stg2d8579c0-ea29-438b-8750-4da72ffc8da0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41572/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 03:51:50,018] [INFO] Task succeeded: Blastn
[2023-03-17 03:51:50,018] [INFO] Selected 12 target genomes.
[2023-03-17 03:51:50,019] [INFO] Target genome list was writen to OceanDNA-b41572/target_genomes_gtdb.txt
[2023-03-17 03:51:50,112] [INFO] Task started: fastANI
[2023-03-17 03:51:50,112] [INFO] Running command: fastANI --query /var/lib/cwl/stg77d54b8c-9ad2-49de-852a-52a4ed72f6c0/OceanDNA-b41572.fa --refList OceanDNA-b41572/target_genomes_gtdb.txt --output OceanDNA-b41572/fastani_result_gtdb.tsv --threads 1
[2023-03-17 03:51:58,467] [INFO] Task succeeded: fastANI
[2023-03-17 03:51:58,474] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 03:51:58,474] [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_002915595.1	s__Marortus luteolus	97.3887	1086	1253	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Marortus	95.0	97.55	97.55	0.86	0.86	2	conclusive
GCF_902705855.1	s__Marortus aliphaticivorans_B	87.706	1009	1253	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Marortus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018066965.1	s__Marortus sp018066965	82.6188	730	1253	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Marortus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018067195.1	s__Marortus sp018067195	80.7825	575	1253	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Marortus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902705875.1	s__Marortus aliphaticivorans_A	79.8911	447	1253	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Marortus	95.0	100.00	100.00	0.99	0.99	2	-
GCF_001586255.1	s__Zhongshania aliphaticivorans	79.4706	379	1253	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Zhongshania	95.0	99.39	99.39	0.94	0.94	2	-
GCF_014202945.1	s__Zhongshania antarctica	79.0435	376	1253	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Zhongshania	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001010805.1	s__IMCC21906 sp001010805	78.2133	160	1253	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__IMCC21906	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014705705.1	s__KMU-158 sp014705705	77.0992	172	1253	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__KMU-158	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000420325.1	s__Spongiibacter tropicus	77.0869	142	1253	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Spongiibacter	95.0	98.00	97.89	0.92	0.88	9	-
--------------------------------------------------------------------------------
[2023-03-17 03:51:58,474] [INFO] GTDB search result was written to OceanDNA-b41572/result_gtdb.tsv
[2023-03-17 03:51:58,475] [INFO] ===== GTDB Search completed =====
[2023-03-17 03:51:58,476] [INFO] DFAST_QC result json was written to OceanDNA-b41572/dqc_result.json
[2023-03-17 03:51:58,476] [INFO] DFAST_QC completed!
[2023-03-17 03:51:58,476] [INFO] Total running time: 0h1m43s