[2023-03-15 07:03:38,786] [INFO] DFAST_QC pipeline started.
[2023-03-15 07:03:38,786] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 07:03:38,786] [INFO] DQC Reference Directory: /var/lib/cwl/stge74bdb48-82da-4623-a6ca-28b0d8881250/dqc_reference
[2023-03-15 07:03:39,906] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 07:03:39,906] [INFO] Task started: Prodigal
[2023-03-15 07:03:39,906] [INFO] Running command: cat /var/lib/cwl/stg27bb3927-c1e8-41b5-9071-348c008caa07/OceanDNA-b26714.fa | prodigal -d OceanDNA-b26714/cds.fna -a OceanDNA-b26714/protein.faa -g 11 -q > /dev/null
[2023-03-15 07:04:01,484] [INFO] Task succeeded: Prodigal
[2023-03-15 07:04:01,484] [INFO] Task started: HMMsearch
[2023-03-15 07:04:01,484] [INFO] Running command: hmmsearch --tblout OceanDNA-b26714/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge74bdb48-82da-4623-a6ca-28b0d8881250/dqc_reference/reference_markers.hmm OceanDNA-b26714/protein.faa > /dev/null
[2023-03-15 07:04:01,702] [INFO] Task succeeded: HMMsearch
[2023-03-15 07:04:01,703] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg27bb3927-c1e8-41b5-9071-348c008caa07/OceanDNA-b26714.fa]
[2023-03-15 07:04:01,762] [INFO] Query marker FASTA was written to OceanDNA-b26714/markers.fasta
[2023-03-15 07:04:01,763] [INFO] Task started: Blastn
[2023-03-15 07:04:01,764] [INFO] Running command: blastn -query OceanDNA-b26714/markers.fasta -db /var/lib/cwl/stge74bdb48-82da-4623-a6ca-28b0d8881250/dqc_reference/reference_markers.fasta -out OceanDNA-b26714/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:04:02,385] [INFO] Task succeeded: Blastn
[2023-03-15 07:04:02,391] [INFO] Selected 14 target genomes.
[2023-03-15 07:04:02,391] [INFO] Target genome list was writen to OceanDNA-b26714/target_genomes.txt
[2023-03-15 07:04:02,398] [INFO] Task started: fastANI
[2023-03-15 07:04:02,398] [INFO] Running command: fastANI --query /var/lib/cwl/stg27bb3927-c1e8-41b5-9071-348c008caa07/OceanDNA-b26714.fa --refList OceanDNA-b26714/target_genomes.txt --output OceanDNA-b26714/fastani_result.tsv --threads 1
[2023-03-15 07:04:12,625] [INFO] Task succeeded: fastANI
[2023-03-15 07:04:12,625] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge74bdb48-82da-4623-a6ca-28b0d8881250/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 07:04:12,625] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge74bdb48-82da-4623-a6ca-28b0d8881250/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 07:04:12,634] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 07:04:12,634] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 07:04:12,634] [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
Pelagibacterium halotolerans	strain=B2	GCA_000230555.1	531813	531813	type	True	86.9399	832	1139	95	below_threshold
Pelagibacterium lacus	strain=XYN52	GCA_003345525.1	2282655	2282655	type	True	80.2955	512	1139	95	below_threshold
Pelagibacterium luteolum	strain=CGMCC 1.10267	GCA_900100665.1	440168	440168	type	True	80.0141	524	1139	95	below_threshold
Pelagibacterium sediminicola	strain=IMCC34151	GCA_003390885.1	2248761	2248761	type	True	79.1506	448	1139	95	below_threshold
Pelagibacterium xiamenense	strain=HS1C4-1	GCA_021166475.1	2901140	2901140	type	True	78.6148	398	1139	95	below_threshold
Pelagibacterium montanilacus	strain=CCL18	GCA_003992665.1	2185280	2185280	type	True	78.5262	369	1139	95	below_threshold
Pelagibacterium limicola	strain=NAJP-14	GCA_015694405.1	2791022	2791022	type	True	78.2889	403	1139	95	below_threshold
Pelagibacterium lentulum	strain=B2	GCA_003992625.1	2029865	2029865	type	True	78.1753	353	1139	95	below_threshold
Devosia beringensis	strain=S02	GCA_014926585.1	2657486	2657486	type	True	77.4329	262	1139	95	below_threshold
Devosia oryziradicis	strain=G19	GCA_016698645.1	2801335	2801335	type	True	77.036	236	1139	95	below_threshold
Cucumibacter marinus	strain=DSM 18995	GCA_000429865.1	1121252	1121252	type	True	76.9556	195	1139	95	below_threshold
Rhizobium croatiense	strain=13T	GCA_019793465.1	2867516	2867516	type	True	76.4692	121	1139	95	below_threshold
Microvirga guangxiensis	strain=CGMCC 1.7666	GCA_900102135.1	549386	549386	type	True	76.0098	75	1139	95	below_threshold
Microvirga pakistanensis	strain=NCCP-1258	GCA_004458765.1	1682650	1682650	type	True	75.933	86	1139	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 07:04:12,637] [INFO] DFAST Taxonomy check result was written to OceanDNA-b26714/tc_result.tsv
[2023-03-15 07:04:12,641] [INFO] ===== Taxonomy check completed =====
[2023-03-15 07:04:12,641] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 07:04:12,641] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge74bdb48-82da-4623-a6ca-28b0d8881250/dqc_reference/checkm_data
[2023-03-15 07:04:12,642] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 07:04:12,653] [INFO] Task started: CheckM
[2023-03-15 07:04:12,653] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b26714/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b26714/checkm_input OceanDNA-b26714/checkm_result
[2023-03-15 07:05:06,295] [INFO] Task succeeded: CheckM
[2023-03-15 07:05:06,295] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 07:05:06,317] [INFO] ===== Completeness check finished =====
[2023-03-15 07:05:06,317] [INFO] ===== Start GTDB Search =====
[2023-03-15 07:05:06,317] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b26714/markers.fasta)
[2023-03-15 07:05:06,318] [INFO] Task started: Blastn
[2023-03-15 07:05:06,318] [INFO] Running command: blastn -query OceanDNA-b26714/markers.fasta -db /var/lib/cwl/stge74bdb48-82da-4623-a6ca-28b0d8881250/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b26714/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 07:05:07,277] [INFO] Task succeeded: Blastn
[2023-03-15 07:05:07,279] [INFO] Selected 9 target genomes.
[2023-03-15 07:05:07,279] [INFO] Target genome list was writen to OceanDNA-b26714/target_genomes_gtdb.txt
[2023-03-15 07:05:07,374] [INFO] Task started: fastANI
[2023-03-15 07:05:07,374] [INFO] Running command: fastANI --query /var/lib/cwl/stg27bb3927-c1e8-41b5-9071-348c008caa07/OceanDNA-b26714.fa --refList OceanDNA-b26714/target_genomes_gtdb.txt --output OceanDNA-b26714/fastani_result_gtdb.tsv --threads 1
[2023-03-15 07:05:14,817] [INFO] Task succeeded: fastANI
[2023-03-15 07:05:14,823] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 07:05:14,823] [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
GCA_002375765.1	s__Pelagibacterium sp002375765	99.856	1075	1139	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	99.84	99.84	0.95	0.95	2	conclusive
GCA_002723255.1	s__Pelagibacterium sp002723255	87.5096	699	1139	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	98.69	98.23	0.81	0.73	4	-
GCF_000230555.1	s__Pelagibacterium halotolerans	86.9208	833	1139	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	99.99	99.99	1.00	1.00	3	-
GCA_002337455.1	s__Pelagibacterium sp002337455	86.4171	852	1139	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	99.90	99.87	0.93	0.91	4	-
GCF_003345525.1	s__Pelagibacterium lacus	80.3121	511	1139	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100665.1	s__Pelagibacterium luteolum	80.0387	521	1139	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003992665.1	s__Pelagibacterium montanilacus	78.51	371	1139	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015694405.1	s__Pelagibacterium limicola	78.2991	402	1139	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Pelagibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001427605.1	s__Devosia sp001427605	77.4077	264	1139	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Devosiaceae;g__Devosia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 07:05:14,827] [INFO] GTDB search result was written to OceanDNA-b26714/result_gtdb.tsv
[2023-03-15 07:05:14,829] [INFO] ===== GTDB Search completed =====
[2023-03-15 07:05:14,832] [INFO] DFAST_QC result json was written to OceanDNA-b26714/dqc_result.json
[2023-03-15 07:05:14,833] [INFO] DFAST_QC completed!
[2023-03-15 07:05:14,833] [INFO] Total running time: 0h1m36s