[2023-03-16 17:28:07,355] [INFO] DFAST_QC pipeline started.
[2023-03-16 17:28:07,356] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 17:28:07,356] [INFO] DQC Reference Directory: /var/lib/cwl/stgd517dd69-0790-4198-bd1a-b946e3776834/dqc_reference
[2023-03-16 17:28:09,213] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 17:28:09,214] [INFO] Task started: Prodigal
[2023-03-16 17:28:09,214] [INFO] Running command: cat /var/lib/cwl/stg76349fb6-760f-47db-9ac8-149eef7b906d/OceanDNA-b17267.fa | prodigal -d OceanDNA-b17267/cds.fna -a OceanDNA-b17267/protein.faa -g 11 -q > /dev/null
[2023-03-16 17:28:32,468] [INFO] Task succeeded: Prodigal
[2023-03-16 17:28:32,469] [INFO] Task started: HMMsearch
[2023-03-16 17:28:32,469] [INFO] Running command: hmmsearch --tblout OceanDNA-b17267/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd517dd69-0790-4198-bd1a-b946e3776834/dqc_reference/reference_markers.hmm OceanDNA-b17267/protein.faa > /dev/null
[2023-03-16 17:28:32,917] [INFO] Task succeeded: HMMsearch
[2023-03-16 17:28:32,918] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg76349fb6-760f-47db-9ac8-149eef7b906d/OceanDNA-b17267.fa]
[2023-03-16 17:28:32,952] [INFO] Query marker FASTA was written to OceanDNA-b17267/markers.fasta
[2023-03-16 17:28:32,956] [INFO] Task started: Blastn
[2023-03-16 17:28:32,956] [INFO] Running command: blastn -query OceanDNA-b17267/markers.fasta -db /var/lib/cwl/stgd517dd69-0790-4198-bd1a-b946e3776834/dqc_reference/reference_markers.fasta -out OceanDNA-b17267/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:28:33,597] [INFO] Task succeeded: Blastn
[2023-03-16 17:28:33,598] [INFO] Selected 25 target genomes.
[2023-03-16 17:28:33,598] [INFO] Target genome list was writen to OceanDNA-b17267/target_genomes.txt
[2023-03-16 17:28:33,619] [INFO] Task started: fastANI
[2023-03-16 17:28:33,619] [INFO] Running command: fastANI --query /var/lib/cwl/stg76349fb6-760f-47db-9ac8-149eef7b906d/OceanDNA-b17267.fa --refList OceanDNA-b17267/target_genomes.txt --output OceanDNA-b17267/fastani_result.tsv --threads 1
[2023-03-16 17:28:59,682] [INFO] Task succeeded: fastANI
[2023-03-16 17:28:59,683] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd517dd69-0790-4198-bd1a-b946e3776834/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 17:28:59,683] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd517dd69-0790-4198-bd1a-b946e3776834/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 17:28:59,692] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 17:28:59,692] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 17:28:59,692] [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
Longimicrobium terrae	strain=CB-286315	GCA_013000925.1	1639882	1639882	type	True	75.5329	81	988	95	below_threshold
Longimicrobium terrae	strain=DSM 29007	GCA_014202995.1	1639882	1639882	type	True	75.5192	82	988	95	below_threshold
Longimicrobium terrae	strain=CECT 8660	GCA_014198875.1	1639882	1639882	type	True	75.5192	82	988	95	below_threshold
Gemmatirosa kalamazoonensis	strain=KBS708	GCA_000522985.1	861299	861299	type	True	75.1962	69	988	95	below_threshold
Thioalbus denitrificans	strain=DSM 26407	GCA_003337735.1	547122	547122	type	True	74.8194	55	988	95	below_threshold
Jiangella mangrovi	strain=DSM 102122	GCA_014204975.1	1524084	1524084	type	True	74.793	60	988	95	below_threshold
Jiangella ureilytica	strain=KC603	GCA_004348545.1	2530374	2530374	type	True	74.6636	61	988	95	below_threshold
Streptomyces coeruleorubidus	strain=JCM 4359	GCA_014649455.1	116188	116188	suspected-type	True	74.6574	72	988	95	below_threshold
Streptomyces coeruleorubidus	strain=ATCC 13740	GCA_008705135.1	116188	116188	suspected-type	True	74.6558	73	988	95	below_threshold
Streptomyces africanus	strain=NRRL B-24243	GCA_002150735.1	231024	231024	type	True	74.5597	63	988	95	below_threshold
Streptosporangium pseudovulgare	strain=JCM 3115	GCA_014648055.1	35765	35765	type	True	74.5499	76	988	95	below_threshold
Streptosporangium sandarakinum	strain=DSM 45763	GCA_013409935.1	1260955	1260955	type	True	74.5198	69	988	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 17:28:59,693] [INFO] DFAST Taxonomy check result was written to OceanDNA-b17267/tc_result.tsv
[2023-03-16 17:28:59,693] [INFO] ===== Taxonomy check completed =====
[2023-03-16 17:28:59,694] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 17:28:59,694] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd517dd69-0790-4198-bd1a-b946e3776834/dqc_reference/checkm_data
[2023-03-16 17:28:59,695] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 17:28:59,726] [INFO] Task started: CheckM
[2023-03-16 17:28:59,726] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b17267/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b17267/checkm_input OceanDNA-b17267/checkm_result
[2023-03-16 17:29:50,671] [INFO] Task succeeded: CheckM
[2023-03-16 17:29:50,671] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.61%
Contamintation: 9.23%
Strain heterogeneity: 25.00%
--------------------------------------------------------------------------------
[2023-03-16 17:29:50,676] [INFO] ===== Completeness check finished =====
[2023-03-16 17:29:50,676] [INFO] ===== Start GTDB Search =====
[2023-03-16 17:29:50,676] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b17267/markers.fasta)
[2023-03-16 17:29:50,678] [INFO] Task started: Blastn
[2023-03-16 17:29:50,678] [INFO] Running command: blastn -query OceanDNA-b17267/markers.fasta -db /var/lib/cwl/stgd517dd69-0790-4198-bd1a-b946e3776834/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b17267/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 17:29:51,493] [INFO] Task succeeded: Blastn
[2023-03-16 17:29:51,495] [INFO] Selected 21 target genomes.
[2023-03-16 17:29:51,495] [INFO] Target genome list was writen to OceanDNA-b17267/target_genomes_gtdb.txt
[2023-03-16 17:29:51,528] [INFO] Task started: fastANI
[2023-03-16 17:29:51,528] [INFO] Running command: fastANI --query /var/lib/cwl/stg76349fb6-760f-47db-9ac8-149eef7b906d/OceanDNA-b17267.fa --refList OceanDNA-b17267/target_genomes_gtdb.txt --output OceanDNA-b17267/fastani_result_gtdb.tsv --threads 1
[2023-03-16 17:30:03,495] [INFO] Task succeeded: fastANI
[2023-03-16 17:30:03,505] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 17:30:03,506] [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_015492755.1	s__S146-37 sp015492755	78.3084	186	988	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__S146-37	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007120305.1	s__SKNW01 sp007120305	76.9943	79	988	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__SKNW01	95.0	99.60	99.60	0.85	0.85	2	-
GCA_007695195.1	s__PWLA01 sp007695195	76.9148	121	988	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__PWLA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003248075.1	s__SZUA-318 sp003248075	76.8786	232	988	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__SZUA-318	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016873995.1	s__UBA2982 sp016873995	76.8009	86	988	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__UBA2982	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007692505.1	s__REBX01 sp007692505	76.7131	142	988	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__REBX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013002885.1	s__UBA2589 sp013002885	76.6868	135	988	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__UBA2589	95.0	99.00	99.00	0.85	0.85	2	-
GCA_007695225.1	s__T3Sed10-66 sp003564555	76.6501	139	988	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__T3Sed10-66	95.0	96.43	96.28	0.79	0.76	4	-
GCA_007132965.1	s__PWLA01 sp007132965	76.6432	121	988	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__PWLA01	95.0	99.78	99.76	0.93	0.93	3	-
GCA_003564295.1	s__PXFI01 sp003564295	76.6234	84	988	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__PXFI01	95.0	95.78	95.56	0.60	0.59	3	-
GCA_003559555.1	s__PWLA01 sp003559555	76.4784	132	988	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__PWLA01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007692665.1	s__SKNW01 sp007692665	76.4474	118	988	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__SKNW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018678395.1	s__IDS-52 sp018678395	76.4083	85	988	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__IDS-52	95.0	98.28	98.28	0.76	0.76	2	-
GCA_007122885.1	s__SKSR01 sp007122885	76.2835	73	988	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__SKSR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003695865.1	s__J028 sp003695865	76.1107	86	988	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__J028	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007126035.1	s__SLCC01 sp007126035	76.0231	90	988	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__RSA9;g__SLCC01	95.0	99.93	99.93	0.94	0.94	2	-
GCA_002238865.1	s__Bin94 sp002238865	75.7607	79	988	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__Bin94	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 17:30:03,507] [INFO] GTDB search result was written to OceanDNA-b17267/result_gtdb.tsv
[2023-03-16 17:30:03,508] [INFO] ===== GTDB Search completed =====
[2023-03-16 17:30:03,511] [INFO] DFAST_QC result json was written to OceanDNA-b17267/dqc_result.json
[2023-03-16 17:30:03,511] [INFO] DFAST_QC completed!
[2023-03-16 17:30:03,511] [INFO] Total running time: 0h1m56s