[2023-03-18 07:06:20,691] [INFO] DFAST_QC pipeline started.
[2023-03-18 07:06:20,691] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 07:06:20,691] [INFO] DQC Reference Directory: /var/lib/cwl/stgd8f02b3f-fcad-4c44-b51e-f816defb2702/dqc_reference
[2023-03-18 07:06:22,302] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 07:06:22,303] [INFO] Task started: Prodigal
[2023-03-18 07:06:22,303] [INFO] Running command: cat /var/lib/cwl/stgd09448b8-1900-4f51-872e-9e6a0b2ec2f1/OceanDNA-b7455.fa | prodigal -d OceanDNA-b7455/cds.fna -a OceanDNA-b7455/protein.faa -g 11 -q > /dev/null
[2023-03-18 07:06:35,838] [INFO] Task succeeded: Prodigal
[2023-03-18 07:06:35,839] [INFO] Task started: HMMsearch
[2023-03-18 07:06:35,839] [INFO] Running command: hmmsearch --tblout OceanDNA-b7455/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd8f02b3f-fcad-4c44-b51e-f816defb2702/dqc_reference/reference_markers.hmm OceanDNA-b7455/protein.faa > /dev/null
[2023-03-18 07:06:36,018] [INFO] Task succeeded: HMMsearch
[2023-03-18 07:06:36,018] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd09448b8-1900-4f51-872e-9e6a0b2ec2f1/OceanDNA-b7455.fa]
[2023-03-18 07:06:36,031] [INFO] Query marker FASTA was written to OceanDNA-b7455/markers.fasta
[2023-03-18 07:06:36,031] [INFO] Task started: Blastn
[2023-03-18 07:06:36,031] [INFO] Running command: blastn -query OceanDNA-b7455/markers.fasta -db /var/lib/cwl/stgd8f02b3f-fcad-4c44-b51e-f816defb2702/dqc_reference/reference_markers.fasta -out OceanDNA-b7455/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:06:36,586] [INFO] Task succeeded: Blastn
[2023-03-18 07:06:36,586] [INFO] Selected 25 target genomes.
[2023-03-18 07:06:36,587] [INFO] Target genome list was writen to OceanDNA-b7455/target_genomes.txt
[2023-03-18 07:06:36,598] [INFO] Task started: fastANI
[2023-03-18 07:06:36,598] [INFO] Running command: fastANI --query /var/lib/cwl/stgd09448b8-1900-4f51-872e-9e6a0b2ec2f1/OceanDNA-b7455.fa --refList OceanDNA-b7455/target_genomes.txt --output OceanDNA-b7455/fastani_result.tsv --threads 1
[2023-03-18 07:06:49,515] [INFO] Task succeeded: fastANI
[2023-03-18 07:06:49,516] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd8f02b3f-fcad-4c44-b51e-f816defb2702/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 07:06:49,516] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd8f02b3f-fcad-4c44-b51e-f816defb2702/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 07:06:49,529] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 07:06:49,529] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-18 07:06:49,529] [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
Urechidicola croceus	strain=LPB0138	GCA_001761325.1	1850246	1850246	type	True	78.2007	308	727	95	below_threshold
Polaribacter aquimarinus	strain=ZY113	GCA_003129485.1	2100726	2100726	type	True	77.0878	164	727	95	below_threshold
Polaribacter aestuariivivens	strain=DBTF-3	GCA_005885675.1	2304626	2304626	type	True	76.9965	188	727	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	76.993	198	727	95	below_threshold
Polaribacter sejongensis	strain=KCTC 23670	GCA_002814075.1	985043	985043	type	True	76.9894	176	727	95	below_threshold
Polaribacter haliotis	strain=RA4-7	GCA_002201315.1	1888915	1888915	type	True	76.9727	179	727	95	below_threshold
Polaribacter undariae	strain=KCTC 42175	GCA_024918935.1	1574269	1574269	type	True	76.9614	184	727	95	below_threshold
Tenacibaculum aquimarinum	strain=K20-16	GCA_022478115.1	2910675	2910675	type	True	76.9525	193	727	95	below_threshold
Polaribacter haliotis	strain=KCTC 52418	GCA_014784055.1	1888915	1888915	type	True	76.952	181	727	95	below_threshold
Polaribacter porphyrae	strain=LMG 26671	GCA_020532745.1	1137780	1137780	type	True	76.9472	179	727	95	below_threshold
Polaribacter septentrionalilitoris	strain=ANORD1	GCA_009832745.1	2494657	2494657	type	True	76.9125	180	727	95	below_threshold
Polaribacter porphyrae	strain=NBRC 108759	GCA_002954685.1	1137780	1137780	type	True	76.9033	185	727	95	below_threshold
Polaribacter butkevichii	strain=KCTC 12100	GCA_002954605.1	218490	218490	type	True	76.8643	176	727	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_001680875.1	996801	996801	type	True	76.8465	183	727	95	below_threshold
Polaribacter reichenbachii	strain=6Alg 8T	GCA_001975665.1	996801	996801	type	True	76.8335	187	727	95	below_threshold
Polaribacter reichenbachii	strain=KCTC 23969	GCA_002814055.1	996801	996801	type	True	76.8198	184	727	95	below_threshold
Lutibacter agarilyticus	strain=DSM 29150	GCA_900188235.1	1109740	1109740	type	True	76.8023	153	727	95	below_threshold
Polaribacter reichenbachii	strain=LMG 26443	GCA_020532845.1	996801	996801	type	True	76.7655	184	727	95	below_threshold
Polaribacter dokdonensis	strain=KCTC 12392	GCA_024362345.1	326329	326329	type	True	76.7597	154	727	95	below_threshold
Polaribacter dokdonensis	strain=DSW-5	GCA_900106865.1	326329	326329	type	True	76.7397	152	727	95	below_threshold
Polaribacter dokdonensis	strain=DSW-5	GCA_001280865.1	326329	326329	type	True	76.7314	156	727	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	76.7216	176	727	95	below_threshold
Lutibacter flavus	strain=DSM 27993	GCA_900188355.1	691689	691689	type	True	76.6111	178	727	95	below_threshold
Polaribacter litorisediminis	strain=OITF-11	GCA_019968605.1	1908341	1908341	type	True	76.391	142	727	95	below_threshold
Aureibaculum algae	strain=10Alg 115	GCA_006065315.1	2584122	2584122	type	True	76.3144	116	727	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-18 07:06:49,530] [INFO] DFAST Taxonomy check result was written to OceanDNA-b7455/tc_result.tsv
[2023-03-18 07:06:49,530] [INFO] ===== Taxonomy check completed =====
[2023-03-18 07:06:49,530] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 07:06:49,530] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd8f02b3f-fcad-4c44-b51e-f816defb2702/dqc_reference/checkm_data
[2023-03-18 07:06:49,531] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 07:06:49,534] [INFO] Task started: CheckM
[2023-03-18 07:06:49,534] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b7455/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b7455/checkm_input OceanDNA-b7455/checkm_result
[2023-03-18 07:07:26,335] [INFO] Task succeeded: CheckM
[2023-03-18 07:07:26,335] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 07:07:26,337] [INFO] ===== Completeness check finished =====
[2023-03-18 07:07:26,337] [INFO] ===== Start GTDB Search =====
[2023-03-18 07:07:26,338] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b7455/markers.fasta)
[2023-03-18 07:07:26,338] [INFO] Task started: Blastn
[2023-03-18 07:07:26,338] [INFO] Running command: blastn -query OceanDNA-b7455/markers.fasta -db /var/lib/cwl/stgd8f02b3f-fcad-4c44-b51e-f816defb2702/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b7455/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 07:07:27,142] [INFO] Task succeeded: Blastn
[2023-03-18 07:07:27,143] [INFO] Selected 21 target genomes.
[2023-03-18 07:07:27,143] [INFO] Target genome list was writen to OceanDNA-b7455/target_genomes_gtdb.txt
[2023-03-18 07:07:27,396] [INFO] Task started: fastANI
[2023-03-18 07:07:27,396] [INFO] Running command: fastANI --query /var/lib/cwl/stgd09448b8-1900-4f51-872e-9e6a0b2ec2f1/OceanDNA-b7455.fa --refList OceanDNA-b7455/target_genomes_gtdb.txt --output OceanDNA-b7455/fastani_result_gtdb.tsv --threads 1
[2023-03-18 07:07:39,729] [INFO] Task succeeded: fastANI
[2023-03-18 07:07:39,740] [INFO] Found 21 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 07:07:39,741] [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_002733665.1	s__Urechidicola sp002733665	80.002	408	727	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Urechidicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905479835.1	s__Urechidicola sp905479835	78.9332	272	727	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Urechidicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001761325.1	s__Urechidicola croceus	78.2128	307	727	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Urechidicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905181865.1	s__Urechidicola croceus_A	77.6226	151	727	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Urechidicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016744415.1	s__Urechidicola sp016744415	77.5182	223	727	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Urechidicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001874265.1	s__Urechidicola sp001874265	77.2035	179	727	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Urechidicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002163675.1	s__Polaribacter sp002163675	77.1693	200	727	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003129485.1	s__Polaribacter sp003129485	77.0873	164	727	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002814075.1	s__Polaribacter sejongensis	76.9894	176	727	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	97.48	97.48	0.89	0.89	2	-
GCA_905480405.1	s__Polaribacter sp905480405	76.8913	174	727	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002954605.1	s__Polaribacter butkevichii	76.8643	176	727	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001693415.1	s__Tenacibaculum soleae	76.8566	170	727	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001975665.1	s__Polaribacter reichenbachii	76.8211	188	727	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	99.98	99.97	1.00	1.00	3	-
GCF_003260195.1	s__Lutibacter citreus	76.7526	178	727	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009796785.1	s__Polaribacter sp009796785	76.7513	183	727	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001280865.1	s__Polaribacter dokdonensis	76.7314	156	727	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_018861005.1	s__Polaribacter vadi_A	76.6242	196	727	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188355.1	s__Lutibacter flavus	76.6111	178	727	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646675.1	s__Lutibacter litoralis	76.5856	162	727	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_012524075.1	s__Lutibacter sp012524075	76.3494	147	727	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900198195.1	s__Tenacibaculum jejuense	76.2974	139	727	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tenacibaculum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 07:07:39,741] [INFO] GTDB search result was written to OceanDNA-b7455/result_gtdb.tsv
[2023-03-18 07:07:39,741] [INFO] ===== GTDB Search completed =====
[2023-03-18 07:07:39,743] [INFO] DFAST_QC result json was written to OceanDNA-b7455/dqc_result.json
[2023-03-18 07:07:39,743] [INFO] DFAST_QC completed!
[2023-03-18 07:07:39,743] [INFO] Total running time: 0h1m19s