[2023-03-18 21:43:12,553] [INFO] DFAST_QC pipeline started.
[2023-03-18 21:43:12,553] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 21:43:12,554] [INFO] DQC Reference Directory: /var/lib/cwl/stg78a4926c-fd8b-4147-8305-8ccd9c3bb7a7/dqc_reference
[2023-03-18 21:43:13,668] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 21:43:13,668] [INFO] Task started: Prodigal
[2023-03-18 21:43:13,668] [INFO] Running command: cat /var/lib/cwl/stgeb6798c1-84e0-48f4-b846-3ab2fdd26683/OceanDNA-b30217.fa | prodigal -d OceanDNA-b30217/cds.fna -a OceanDNA-b30217/protein.faa -g 11 -q > /dev/null
[2023-03-18 21:43:38,925] [INFO] Task succeeded: Prodigal
[2023-03-18 21:43:38,926] [INFO] Task started: HMMsearch
[2023-03-18 21:43:38,926] [INFO] Running command: hmmsearch --tblout OceanDNA-b30217/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg78a4926c-fd8b-4147-8305-8ccd9c3bb7a7/dqc_reference/reference_markers.hmm OceanDNA-b30217/protein.faa > /dev/null
[2023-03-18 21:43:39,127] [INFO] Task succeeded: HMMsearch
[2023-03-18 21:43:39,128] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgeb6798c1-84e0-48f4-b846-3ab2fdd26683/OceanDNA-b30217.fa]
[2023-03-18 21:43:39,153] [INFO] Query marker FASTA was written to OceanDNA-b30217/markers.fasta
[2023-03-18 21:43:39,154] [INFO] Task started: Blastn
[2023-03-18 21:43:39,154] [INFO] Running command: blastn -query OceanDNA-b30217/markers.fasta -db /var/lib/cwl/stg78a4926c-fd8b-4147-8305-8ccd9c3bb7a7/dqc_reference/reference_markers.fasta -out OceanDNA-b30217/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:43:39,822] [INFO] Task succeeded: Blastn
[2023-03-18 21:43:39,823] [INFO] Selected 18 target genomes.
[2023-03-18 21:43:39,823] [INFO] Target genome list was writen to OceanDNA-b30217/target_genomes.txt
[2023-03-18 21:43:39,832] [INFO] Task started: fastANI
[2023-03-18 21:43:39,832] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb6798c1-84e0-48f4-b846-3ab2fdd26683/OceanDNA-b30217.fa --refList OceanDNA-b30217/target_genomes.txt --output OceanDNA-b30217/fastani_result.tsv --threads 1
[2023-03-18 21:43:51,767] [INFO] Task succeeded: fastANI
[2023-03-18 21:43:51,767] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg78a4926c-fd8b-4147-8305-8ccd9c3bb7a7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 21:43:51,767] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg78a4926c-fd8b-4147-8305-8ccd9c3bb7a7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 21:43:51,778] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 21:43:51,778] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 21:43:51,778] [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
Sulfitobacter marinus	strain=DSM 23422	GCA_900116285.1	394264	394264	type	True	81.0195	624	1281	95	below_threshold
Sulfitobacter pontiacus	strain=DSM 10014	GCA_900106935.1	60137	60137	type	True	80.4644	560	1281	95	below_threshold
Sulfitobacter litoralis	strain=DSM 17584	GCA_900103185.1	335975	335975	type	True	79.9134	557	1281	95	below_threshold
Sulfitobacter indolifex	strain=DSM 14862	GCA_022788655.1	225422	225422	type	True	78.156	309	1281	95	below_threshold
Sulfitobacter indolifex	strain=HEL-45	GCA_000172095.1	225422	225422	type	True	78.1228	306	1281	95	below_threshold
Pseudosulfitobacter pseudonitzschiae	strain=H3	GCA_000712315.1	1402135	1402135	type	True	78.054	373	1281	95	below_threshold
Sulfitobacter geojensis	strain=MM-124	GCA_000622325.1	1342299	1342299	type	True	77.9607	389	1281	95	below_threshold
Sulfitobacter mediterraneus	strain=DSM 12244	GCA_003054325.1	83219	83219	type	True	77.9321	392	1281	95	below_threshold
Sulfitobacter geojensis	strain=DSM 101063	GCA_013407805.1	1342299	1342299	type	True	77.8841	408	1281	95	below_threshold
Sulfitobacter noctilucae	strain=NB-68	GCA_000622365.1	1342302	1342302	type	True	77.7001	329	1281	95	below_threshold
Sulfitobacter sabulilitoris	strain=HSMS-29	GCA_005887615.1	2562655	2562655	type	True	77.5693	373	1281	95	below_threshold
Sulfitobacter noctilucicola	strain=NB-77	GCA_000622385.1	1342301	1342301	type	True	77.4905	302	1281	95	below_threshold
Sulfitobacter noctilucicola	strain=DSM 101015	GCA_014197555.1	1342301	1342301	type	True	77.4292	308	1281	95	below_threshold
Roseobacter ponti	strain=DSM 106830	GCA_012932215.1	1891787	1891787	type	True	76.6925	189	1281	95	below_threshold
Alexandriicola marinus	strain=LZ-14	GCA_004000435.1	2081710	2081710	type	True	76.5644	149	1281	95	below_threshold
Rhodovulum tesquicola	strain=A-36s	GCA_024128855.1	540254	540254	type	True	76.3211	137	1281	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_019130055.1	2852097	2852097	type	True	76.2768	136	1281	95	below_threshold
Rhodobacter amnigenus	strain=HSP-20	GCA_009908265.2	2852097	2852097	type	True	76.2768	136	1281	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 21:43:51,778] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30217/tc_result.tsv
[2023-03-18 21:43:51,778] [INFO] ===== Taxonomy check completed =====
[2023-03-18 21:43:51,779] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 21:43:51,779] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg78a4926c-fd8b-4147-8305-8ccd9c3bb7a7/dqc_reference/checkm_data
[2023-03-18 21:43:51,779] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 21:43:51,784] [INFO] Task started: CheckM
[2023-03-18 21:43:51,785] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30217/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30217/checkm_input OceanDNA-b30217/checkm_result
[2023-03-18 21:44:54,160] [INFO] Task succeeded: CheckM
[2023-03-18 21:44:54,161] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 69.27%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 21:44:54,164] [INFO] ===== Completeness check finished =====
[2023-03-18 21:44:54,164] [INFO] ===== Start GTDB Search =====
[2023-03-18 21:44:54,165] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30217/markers.fasta)
[2023-03-18 21:44:54,165] [INFO] Task started: Blastn
[2023-03-18 21:44:54,165] [INFO] Running command: blastn -query OceanDNA-b30217/markers.fasta -db /var/lib/cwl/stg78a4926c-fd8b-4147-8305-8ccd9c3bb7a7/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30217/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 21:44:55,364] [INFO] Task succeeded: Blastn
[2023-03-18 21:44:55,364] [INFO] Selected 14 target genomes.
[2023-03-18 21:44:55,365] [INFO] Target genome list was writen to OceanDNA-b30217/target_genomes_gtdb.txt
[2023-03-18 21:44:55,374] [INFO] Task started: fastANI
[2023-03-18 21:44:55,374] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb6798c1-84e0-48f4-b846-3ab2fdd26683/OceanDNA-b30217.fa --refList OceanDNA-b30217/target_genomes_gtdb.txt --output OceanDNA-b30217/fastani_result_gtdb.tsv --threads 1
[2023-03-18 21:45:06,101] [INFO] Task succeeded: fastANI
[2023-03-18 21:45:06,110] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 21:45:06,110] [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_000156335.1	s__Sulfitobacter sp000156335	85.2781	918	1281	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013282155.1	s__Sulfitobacter sp013282155	82.8394	712	1281	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	99.41	99.36	0.93	0.90	3	-
GCA_013139555.1	s__Sulfitobacter sp013139555	81.7568	547	1281	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116285.1	s__Sulfitobacter marinus	81.0155	624	1281	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106935.1	s__Sulfitobacter pontiacus	80.4644	560	1281	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	97.43	97.01	0.92	0.86	24	-
GCF_006064855.1	s__Sulfitobacter sp006064855	80.1905	522	1281	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103185.1	s__Sulfitobacter litoralis	79.9134	557	1281	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	99.10	98.53	0.92	0.85	6	-
GCA_002731875.1	s__Sulfitobacter sp002731875	78.7649	436	1281	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	99.91	99.88	0.91	0.87	3	-
GCF_003335585.1	s__Sulfitobacter sp003335585	78.3781	457	1281	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001650875.1	s__Sulfitobacter sp001650875	78.1794	423	1281	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003352065.1	s__Sulfitobacter sp003352065	77.8618	347	1281	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000620505.1	s__Ascidiaceihabitans sp000620505	77.8609	390	1281	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Ascidiaceihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000622365.1	s__Sulfitobacter noctilucae	77.7001	329	1281	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Sulfitobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012932215.1	s__Roseobacter ponti	76.6925	189	1281	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 21:45:06,110] [INFO] GTDB search result was written to OceanDNA-b30217/result_gtdb.tsv
[2023-03-18 21:45:06,110] [INFO] ===== GTDB Search completed =====
[2023-03-18 21:45:06,112] [INFO] DFAST_QC result json was written to OceanDNA-b30217/dqc_result.json
[2023-03-18 21:45:06,112] [INFO] DFAST_QC completed!
[2023-03-18 21:45:06,112] [INFO] Total running time: 0h1m54s