[2023-03-15 07:52:40,312] [INFO] DFAST_QC pipeline started.
[2023-03-15 07:52:40,312] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 07:52:40,312] [INFO] DQC Reference Directory: /var/lib/cwl/stg84d551bc-f936-4cf7-99b1-909b145a0726/dqc_reference
[2023-03-15 07:52:41,432] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 07:52:41,432] [INFO] Task started: Prodigal
[2023-03-15 07:52:41,432] [INFO] Running command: cat /var/lib/cwl/stgfc102c81-8349-45fc-be02-13b412f7a7d0/OceanDNA-b41553.fa | prodigal -d OceanDNA-b41553/cds.fna -a OceanDNA-b41553/protein.faa -g 11 -q > /dev/null
[2023-03-15 07:53:05,170] [INFO] Task succeeded: Prodigal
[2023-03-15 07:53:05,170] [INFO] Task started: HMMsearch
[2023-03-15 07:53:05,170] [INFO] Running command: hmmsearch --tblout OceanDNA-b41553/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg84d551bc-f936-4cf7-99b1-909b145a0726/dqc_reference/reference_markers.hmm OceanDNA-b41553/protein.faa > /dev/null
[2023-03-15 07:53:05,461] [INFO] Task succeeded: HMMsearch
[2023-03-15 07:53:05,461] [INFO] Found 6/6 markers.
[2023-03-15 07:53:05,486] [INFO] Query marker FASTA was written to OceanDNA-b41553/markers.fasta
[2023-03-15 07:53:05,486] [INFO] Task started: Blastn
[2023-03-15 07:53:05,486] [INFO] Running command: blastn -query OceanDNA-b41553/markers.fasta -db /var/lib/cwl/stg84d551bc-f936-4cf7-99b1-909b145a0726/dqc_reference/reference_markers.fasta -out OceanDNA-b41553/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:53:06,152] [INFO] Task succeeded: Blastn
[2023-03-15 07:53:06,153] [INFO] Selected 17 target genomes.
[2023-03-15 07:53:06,153] [INFO] Target genome list was writen to OceanDNA-b41553/target_genomes.txt
[2023-03-15 07:53:06,163] [INFO] Task started: fastANI
[2023-03-15 07:53:06,163] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc102c81-8349-45fc-be02-13b412f7a7d0/OceanDNA-b41553.fa --refList OceanDNA-b41553/target_genomes.txt --output OceanDNA-b41553/fastani_result.tsv --threads 1
[2023-03-15 07:53:18,827] [INFO] Task succeeded: fastANI
[2023-03-15 07:53:18,827] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg84d551bc-f936-4cf7-99b1-909b145a0726/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 07:53:18,827] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg84d551bc-f936-4cf7-99b1-909b145a0726/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 07:53:18,832] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2023-03-15 07:53:18,833] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-03-15 07:53:18,833] [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	97.9637	1195	1348	95	conclusive
Zhongshania antarctica	strain=DSM 25701	GCA_014202945.1	641702	641702	type	True	92.3992	1060	1348	95	below_threshold
Zhongshania antarctica	strain=ZS5-23	GCA_014898265.1	641702	641702	type	True	92.3866	1050	1348	95	below_threshold
Spongiibacter thalassae	strain=KMU-166	GCA_012272835.1	2721624	2721624	type	True	77.3559	194	1348	95	below_threshold
Spongiibacter tropicus	strain=DSM 19543	GCA_000420325.1	454602	454602	type	True	76.925	146	1348	95	below_threshold
Spongiibacter pelagi	strain=KMU-158	GCA_014705705.1	2760804	2760804	type	True	76.8682	171	1348	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 07:53:18,833] [INFO] DFAST Taxonomy check result was written to OceanDNA-b41553/tc_result.tsv
[2023-03-15 07:53:18,833] [INFO] ===== Taxonomy check completed =====
[2023-03-15 07:53:18,833] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 07:53:18,833] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg84d551bc-f936-4cf7-99b1-909b145a0726/dqc_reference/checkm_data
[2023-03-15 07:53:18,834] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 07:53:18,864] [INFO] Task started: CheckM
[2023-03-15 07:53:18,864] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b41553/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b41553/checkm_input OceanDNA-b41553/checkm_result
[2023-03-15 07:54:17,177] [INFO] Task succeeded: CheckM
[2023-03-15 07:54:17,178] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.27%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 07:54:17,181] [INFO] ===== Completeness check finished =====
[2023-03-15 07:54:17,181] [INFO] ===== Start GTDB Search =====
[2023-03-15 07:54:17,181] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b41553/markers.fasta)
[2023-03-15 07:54:17,182] [INFO] Task started: Blastn
[2023-03-15 07:54:17,182] [INFO] Running command: blastn -query OceanDNA-b41553/markers.fasta -db /var/lib/cwl/stg84d551bc-f936-4cf7-99b1-909b145a0726/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b41553/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:54:18,230] [INFO] Task succeeded: Blastn
[2023-03-15 07:54:18,230] [INFO] Selected 17 target genomes.
[2023-03-15 07:54:18,231] [INFO] Target genome list was writen to OceanDNA-b41553/target_genomes_gtdb.txt
[2023-03-15 07:54:18,270] [INFO] Task started: fastANI
[2023-03-15 07:54:18,270] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc102c81-8349-45fc-be02-13b412f7a7d0/OceanDNA-b41553.fa --refList OceanDNA-b41553/target_genomes_gtdb.txt --output OceanDNA-b41553/fastani_result_gtdb.tsv --threads 1
[2023-03-15 07:54:30,173] [INFO] Task succeeded: fastANI
[2023-03-15 07:54:30,180] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 07:54:30,180] [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_001586255.1	s__Zhongshania aliphaticivorans	97.9603	1195	1348	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Zhongshania	95.0	99.39	99.39	0.94	0.94	2	conclusive
GCF_014202945.1	s__Zhongshania antarctica	92.3822	1061	1348	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Zhongshania	95.0	100.00	100.00	1.00	1.00	2	-
GCF_902705855.1	s__Marortus aliphaticivorans_B	79.0804	369	1348	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	79.0588	258	1348	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Marortus	95.0	100.00	100.00	0.99	0.99	2	-
GCF_002915595.1	s__Marortus luteolus	79.024	357	1348	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Marortus	95.0	97.55	97.55	0.86	0.86	2	-
GCA_018066965.1	s__Marortus sp018066965	78.7825	333	1348	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	78.4422	318	1348	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Marortus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001010805.1	s__IMCC21906 sp001010805	77.6235	163	1348	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__IMCC21906	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012272835.1	s__Spongiibacter sp012272835	77.3559	194	1348	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Spongiibacteraceae;g__Spongiibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014705705.1	s__KMU-158 sp014705705	76.8682	171	1348	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_900120175.1	s__Oceanicoccus sp900120175	75.951	51	1348	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__DSM-21967;g__Oceanicoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 07:54:30,181] [INFO] GTDB search result was written to OceanDNA-b41553/result_gtdb.tsv
[2023-03-15 07:54:30,181] [INFO] ===== GTDB Search completed =====
[2023-03-15 07:54:30,182] [INFO] DFAST_QC result json was written to OceanDNA-b41553/dqc_result.json
[2023-03-15 07:54:30,182] [INFO] DFAST_QC completed!
[2023-03-15 07:54:30,182] [INFO] Total running time: 0h1m50s